I thought that if someone uses

John writes a sentence: "I have finished work two hours ago." He asks Peter to proofread it. Having proofread John's sentence, Peter tells John that the use of the present perfect "have finished" is wrong there because there's the time marker "two hours ago." John replies to him in one of the following ways:

1. I thought that if someone uses a time marker like "two hours ago" in a sentence like mine, then it isn't considered incorrect if they use the present perfect there as well. But I was wrong.

2. I thought that if someone used a time marker like "two hours ago" in a sentence like mine, then it wasn't considered incorrect if they used the present perfect there as well. But I was wrong.

Are both versions acceptable in the context given? If so, do you have a preference?

Yes. They're both very well written.

The first does the job perfectly well.

My only change would be to remove the full stop after "as well" and continue the sentence with "but". I tend to discourage learners from trying to start sentences with "and", "but" and "or".