Trying to fix my credit score. Please help.?

I went over the limit by 30% on one of my credit cards a few years ago. The limit was $ 1000 and I had hit $ 1300. I eventually paid everything off in a few months and the card is still active and in good standing.
I think my credit score is negatively affected by this. In my credit reports, the card is listed under “potentially negative accounts” and the only negative thing about it is the fact that I had gone over the limit.
How can I fix this?
If I get the credit card company to raise my limit to $ 2000, would it cancel out the fact that I had gone over the limit?

Thanks.

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