Yep, I'm aware of these issues and have run into them before. I wrote a post about the negative points of Binance just a few days ago in fact. The way it is now, there's pretty much no way that you're not going to lose a bit of money here and there from the way Binance handles fractionals. I've already collected some 'dust' that I can't sell, trade or withdraw and it definitely sucks.

But until a proper DEX arrives, Binance and Bittrex are what we have. Bittrex is more expensive and Binance makes up for it through these other weird methods :( If you do only small trades, Bittrex is probably better. For big amounts, the trading fees on Binance are better even if you loose fractions of coins here and there