The present perfect indicates that the action took quite some time, or was repeated.
That makes your first three sentences very weird, but not because of the prepositions.
The sentences are strange because you describe actions that should have taken quite a while, but then you indicate a specific moment in time, making that impossible.
If we read the sentences in a context where you indicate the action was repeated (every day, for instance), it was a habit, they make more sense:
I am used to getting up early: I have been going to school by 8 am for years now.
It still is a bit strange though - but that is because I wouldn't say this in any tense. I do not go somewhere by a certain time. I get there or arrive there by 8.
After last months speech about the importance of punctuality most employees have been coming to the office at 9 instead of coming in later.
For some reason, he has been moving furniture around and making noise around 7 pm every evening for the last three weeks. It drives me crazy!
The last sentence works fine, assuming that you mean to ask if she has called several times after 10 am.
After makes it clear there was plenty of time for her to call several times.