My understanding is Bittrex makes tens of Millions each day in profits, their running costs by comparison would only be a fraction of that. The fact that they can't keep up is understandable after a large increase in customers for a short while, but months and months of falling behind without any improvement is ridiculous, especially when they can easily afford the extra cost of staff and training.

Surely they would have created a system that identifies a token sitting in an address that should only hold ethereum and surely they can automate it so it returns the tokens to sender automatically (subtracting a fee to cover gas + 1% cut or something).

Yes it takes time to fix this issue (10 minutes verifying transaction, token address, etc the about 10 minutes to send token back), but not only can they recover the costs from providing support, gas, etc, they should be focusing on getting these funds on their exchange and trade able so they can profit from the trades.