Getting random drops and formatting anomalies when compiling

When I compile my manuscript, last lines are randomly dropped and replaced by blank pages. The blank pages are numbered and have the project title.
Also, the section formatting is also randomly not consistent. Same settings, but suddenly one document will justify right instead of left.
So weird.
Does anyone recognize these problems when compiling? What to do?

Grateful for answers and help!

I don’t know about the alignment issue, but the unrelated blank page glitch you describe is the sort of thing that can often be fixed by turning off widow and orphan protect.