Oh c'mon guys, this is math 101. This happens with so many transactions on a lot of things on a daily life. It's rounding and normal.
OP did transactions with a BOT lower than $1 as per indicated limitations. He probably was hoping that he would not pay transactions fees.
If you are doing that many transactions, just do larger transactions where rounding is in your favor. Why is he making thousands of really small transactions? He's probably just slowing down their system anyway.
I'm on with Bitstamp on this one.
Here's an example where I paid less than 0.5% because of rounding:
I bought 0.08774 BTC and only paid 0.047%
I had a 20 BTC sell order there. Someone (maybe even Bitstamp splitting up orders) bought into that with tiny orders, causing me to pay 6x the fee I am supposed to pay. I had no choice in that matter. When hitting the sell button I agreed to sell at 432.01 at a fee of 0.2% over 20BTC, not 1.16%.