Buy some tests later and ask her to test tonight.
It is possible that the pill may have failed and that it is covering up any signs of pregnancy.
If you test today and again in couple of days and both show negative then Im sure they will be correct. The tests pick up on a pregnancy hormone and if she was pregnant 3 weeks ago the hormone level would be high enough to test for by now.
It could be many things, heat, side effect of pill, a bug.
I can understand why you may be worried about her being on the pill when pregnant so explain that to her and Im sure she'll be happy to test and put your mind at rest. You souns like a very thoughtfull and caring person, hope all goes well