If I input a SEP contribution that's too much, it limits the deduction.   

Ive had people that make too large of a contribution (I give them the exact amount and they round up to the nearest 1000, that kind of thing), we just apply the excess to the next year (assuming they still have SE income)

SEP contributions generally get made once you know how much youre allowed to contribute, Ive never had one that a penalty became involved for over contribution..