Lori, though these side effects were not signaled in the clinical trials, there is subsequent reportage from patients.
Some times adverse symptoms lessen as your body adjusts, but because you've been on Fosamax (alendronate) for three months it is more likely that whatever is in the medication that bothers you, it is building up.
You could check to see if there are interactions with any other medication you are taking. In your situation I would stop the Fosamax and call my medical provider. It may take several weeks for the symptoms to subside.
It is brave to continue a medication that is troublesome, but is it wise?

"The osteoporosis drug alendronate increases the risk for depression more than 14-fold in people aged 65 years and younger, and more than 4-fold in people aged 65 years and older.Feb 17, 2022"