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, malfunctions and hacks.
I'll follow up with a timeline of issues that have cost users millions of dollars.
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
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
4/08/2015 - Bitfinex - Halts Trading - Claims Issue with Post-trade Processing - 15000 Gox BTC Moved, 5000 to Bitfinex - Coincidence?
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
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
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/3l9l6ythe_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
https://www.reddit.com/r/Bitcoin/comments/3pbk88/bitcoin_exchange_cryptsy_may_have_gone_full_mt/
5/11/2015 - OKCoin - Cyber Attack
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
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
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
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/
Useful Links with more Events
Consumers' Research Bitcoin Loss Calculations (since 2010)
Coinbase's Incident History
Now we have some options, namely OpenLedger, which is seeing an increase in volume. Remember if you don't own the private keys, you don't own your crypto.