"and as well" is ugly, but the sentence would be wrong if you deleted "and". Instead, you can just get rid of "as well", which doesn't really seem necessary:
"She is using one crutch for walking and is noticing increasing left knee pain."
Generally speaking, it is not a problem to connect two independent clauses with the word "and", and then also use "as well" in the second clause. In your sentence, I would be happier with "as well" placed at the end.
However, I'm not sure I really understand the point of your sentence. I don't understand the logical connection between the two halves.
Thank you. That is what I thought. I am transcribing medical dictation, and this provider often uses this combination of words. I just thought probably this could be American usage.