You... can't pay them more than once. I've never had the option so I'm not sure, but if that's an option for you, it probably means you missed payments. Or it's just a bug.
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...That just means you have Autopay on. It doesn't mean you're increasing their compliance by overpaying, which you can't do.
If their compliance is going up over time, it's because you're actually doing things to increase it. Paying on time just prevents happiness from decreasing, it never increases compliance.
Are you perhaps confused because you see the extra happiness go up from 0 to 2, and think that's the same as compliance? Happiness contributes to compliance, but it's a different stat.
The thing that contributes the most to compliance is respect. If at any point all of them have positive compliance, that entails you must also have positive respect. If you have negative respect, you can pay on time every time and still have negative compliance for the vast majority of the characters.