Timeline: A List of Recent Issues with Cryptocurrency Exchanges

I would like to point that at that time, there probably wasn't any properly functioning and user friendly decentralized exchange (that I was aware of). Now they're starting to appear.

Decentralized exchanges can prevent most of these issues, mainly database errors and malfunctions.

04/01/2015 - Bitstamp Hacked - 19000 BTC Stolen
https://www.bitstamp.net/article/bitstamp-is-open-for-business-better-than-ever/

15/02/2015 - Bter Hacked - 7170 BTC Stolen
http://www.coindesk.com/bter-bitcoin-stolen-cold-wallet-hack/

02/2015 - Bitfinex - Claims of Potential Frontrunning
https://www.reddit.com/r/BitcoinMarkets/comments/2t3iz5/bitfinex_cso_phillip_g_potter_admits_to_trading/

16/03/2015 - Allcrypt Hacked - 40 BTC stolen
http://themerkle.com/news/allcrypt-bitcoin-exchange-hacked-over-40-btc-in-funds-stolen/

25/03/2015 - Cryptoine Hacked - Hot Wallet Compromised and Emptied - Undisclosed Amount
http://www.zdnet.com/article/bitcoin-exchange-cryptoine-hacked/

05/05/2015 - Ukrainian BTC-TRADE Hacked - 30 BTC stolen
http://forklog.net/ukrainian-bitcoin-exchange-btc-trade-hacked-again/

22/05/2015 - Bitfinex - Hacked - Undisclosed Amount
https://www.cryptocoinsnews.com/breaking-bitcoin-exchange-bitfinex-hot-wallet-hacked/
https://www.reddit.com/r/Bitcoin/comments/36uxxz/bitfinex_has_been_hacked/

01/06/2015 - Blockchain.info - Sends 34 BTC to the Wrong Address
http://www.newsbtc.com/2015/06/01/blockchain-sent-8k-worth-bitcoin-to-wrong-address/

10/07/2015 - OKCoin - DDOS Attack
http://blog.okcoin.com/post/123893357479/regarding-july-10th-ddos-attacks-explanation

21/07/2015 - Igot - DDOS Attacks
https://twitter.com/iGotcom/status/623488879815831552

30/07/2015 - Igot - Scam Accusations - Delayed Withdrawls
http://www.coindesk.com/bitcoin-exchange-igot-challenges-scam-allegations/

18/08/2015 - Bitfinex - Flash Crash and Issues with Margin Trading.
https://soundcloud.com/whaleclub-bitcoin/bitfinex-ceo-recording-after-18082015-flash-crash
https://twitter.com/btcWhaleclub/status/633820388938653697

19/08/2015- CEX.IO - Theft Accusations - Missing Funds from User Accounts due to "Fees"
https://bitcointalk.org/index.php?topic=318010.msg12185497#msg12185497

16/08/2015 - Bitcoinica - New Leads about the 40000 BTC Stolen
https://www.reddit.com/r/Bitcoin/comments/3hzfeb/bitcoinica_theft_of_40k/
https://www.blockseer.com/g/63dtw2vOqka6 https://www.youtube.com/watch?v=AypRF9q0llU

24/08/2015 - Bitfinex - Halts Trading - Claims Issue with Post-trade Processing - 15000 Gox BTC Moved, 5000 to Bitfinex - Coincidence?
https://www.reddit.com/r/BitcoinMarkets/comments/3i5thz/daily_discussion_monday_august_24_2015/cudrtfc
https://www.reddit.com/r/Bitcoin/comments/3i6p5s/15000_coins_from_may_2013_bought_from_gox_moved/
http://btc.blockr.io/tx/info/41d84dccf2487efcca5e35a5ec4a20525d736c4590261fe20a71f8c91962a89e
https://www.blockseer.com/g/n8tcg4pOp92t

24/08/2015 - Igot - Exchange Ceases Trading - Ceased All Public Communications Over 1 Week Ago
http://siliconangle.com/blog/2015/08/24/australian-bitcoin-exchange-igot-ceases-trading-may-have-been-an-indian-based-scam/

25/08/2015 - Bitfinex - Trading Halted - Claims Data Corruption Issues
https://twitter.com/bitfinex/status/636258874606133248

27/08/2015 - Coinbase - Claims of Exchange being Down
https://www.reddit.com/r/Bitcoin/comments/3ijnqd/coinbase_down/
http://i.imgur.com/038663J.png

31/08/2015 - OKCoin - American USD, Litecoin, and Bitcoin Deposits Banned - Regulatory Issues
http://bitcoinist.net/chinese-bitcoin-exchange-okcoin-stops-accepting-american-bitcoin-deposits/

03/09/2015 - Coinbase - Customers Charged Twice - No Refunds
http://altcoinpress.com/2015/09/breaking-coinbase-decides-not-to-refund-customers-in-double-billing-glitch/
http://www.econotimes.com/Coinbase-to-credit-user-accounts-with-bitcoin-in-double-billing-glitch-84870

04/09/2015- Blockchain.info Down - System Maintenance
https://twitter.com/blockchain/status/639815205862641665
http://www.coindesk.com/bitcoin-wallet-provider-blockchain-currently-offline/

17/09/2015 - BitPay - 5000 BTC Stolen
http://qntra.net/2015/09/bitpay-claims-hack-amounting-to-5000-bitcoins/
http://cointelegraph.com/news/115289/bitpay-hacked-for-over-18-million-in-bitcoins
https://twitter.com/BlockSeer/status/644346233612431361
https://www.reddit.com/r/Bitcoin/comments/3l9l6y/the_bitpay_chain_of_events_documented_by_hanover/

17/09/2015 - BitReserve (now Uphold) - Claims of Blocking Withdrawals
https://www.reddit.com/r/Bitcoin/comments/3lbqlk/bitreserve_account_blocked_with_46k_eur/
https://www.reddit.com/r/Bitcoin/comments/3kos8k/public_ticket_to_bitreserveorg_can_not_withdraw/?

20/09/2015 - Cryptsy - "Steals" 0.5% of Every Deposit - Fees Increased - No Prior Notice
https://www.cryptsy.com/pages/fees
https://www.reddit.com/r/Bitcoin/comments/3lnipw/cryptsy_increases_withdrawal_fees_to_05_with_zero/

19/10/2015 - Cryptsy - Claims of Exchange Refusing to Pay Out Users
http://siliconangle.com/blog/2015/10/19/bitcoin-exchange-cryptsy-may-have-gone-full-mt-gox-refuses-to-pay-out-customers/
https://www.reddit.com/r/Bitcoin/comments/3pbk88/bitcoin_exchange_cryptsy_may_have_gone_full_mt/

5/11/2015 - OKCoin - Cyber Attack
http://cointelegraph.com/news/115562/biggest-bitcoin-exchange-okcoin-suffers-cyber-attack-price-plummets

10/11/2015 - OKCoin - Malfunction Causes Liquidation - LTC bought at 1.5CNY, sold at 19CNY
https://www.reddit.com/r/Bitcoin/comments/3sb0dx/regarding_okcoin_ltccny_price_error_resuming/
https://www.reddit.com/r/litecoin/comments/3s96j6/look_okcoin_millions_of_litecoins_dumped/

14/11/2015 - Gemini - Looses Credibility - Trades Reversed
https://www.reddit.com/r/Bitcoin/comments/3ss945/just_got_this_email_from_gemini_about_the_2200/
https://www.reddit.com/r/Bitcoin/comments/3sqjrf/gemini_2200_per_bitcoin_are_they_out_of_bitcoin/

24/11/2015 - Kraken - DDOS Attack
https://twitter.com/krakenfx/status/669302757552074752
http://www.bitcoinfuturesguide.com/bitcoin-blog/kraken-has-received-extortion-letter-suffering-ongoing-ddos-attack-will-not-pay
https://www.reddit.com/r/BitcoinMarkets/comments/3u5few/kraken_experiencing_ongoing_ddos_says_they/

30/11/2015 - Arthur Hayes on Chinese Exchanges - Operating as Shadow Banks
https://www.reddit.com/r/BitcoinMarkets/comments/3uv7lt/arthur_hayes_of_bitmex_only_logical_explanation/
http://www.bitcoinfuturesguide.com/bitcoin-blog/arthur-hayes-of-bitmex-chinese-exchanges-are-operating-as-shadow-banks

03/12/2015 - Gemini - Trade Reversal Could Be Unjustified
http://cointelegraph.com/news/115785/bitcoin-trade-reversal-on-geminicom-could-be-unjustified

05/01/2016 - Cryptsy - Lag Claims - Trade Engine and Withdrawals Paused
https://www.reddit.com/r/Bitcoin/comments/3zm3m7/cryptsy_halts_both_trade_engine_and_withdrawals/
http://www.coindesk.com/altcoin-exchange-cryptsy-takes-trade-engine-offline/

07/01/2016 - BTC-E - DDoS Attack
http://forklog.net/two-exchanges-experienced-ddos-attacks
https://twitter.com/btcecom/status/685125259872354305

08/01/2016 - Bitstamp - DDoS Attack
http://forklog.net/two-exchanges-experienced-ddos-attacks/
https://twitter.com/Bitstamp/status/685398977924206592

09/01/2016 - Bitfinex - Claims of Underpaying Custumers
https://www.reddit.com/r/BitcoinMarkets/comments/401dne/is_bitfinex_underpaying_margin_funding_again/

09/01/2015 - Cryptsy - Finally Goes Rogue?
http://bitcoinist.net/cryptsy-has-moved-out-of-their-building-unannounced-nowhere-to-be-found/
https://www.reddit.com/r/Bitcoin/comments/4050h3/cryptsy_has_moved_out_of_their_building/ http://bitcoinist.net/timeline-cryptsy-disappearance-mystery/

10/01/2015 - Coinbase - Peter Todd Double Spends
https://twitter.com/petertoddbtc/status/686362883756695553
http://bitcoinist.net/peter-todd-double-spends-on-coinbase/

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Useful Links with more Events

Consumers' Research Bitcoin Loss Calculations (since 2010)
Coinbase's Incident History