Your understanding is correct, the fee is for miscellaneous fees that may be charged in addition to the commission. This can be exchange fees, SEC fees, etc.
However I've never heard of it being off like that. If you enter .10, it should remain .10. I have re-confirmed that this is how it works here, and that it displayed in the transaction register as .10. I'm not sure why it's displaying incorrectly for you, but try editing the transaction to correct it.