I have experienced the same issue for the past few weeks. In my case, it seems to be a random selection of which line to delete, and more often than not, it is not the line I selected. The work-around I am using is to "Save" (but not close) the entry, then delete the line and "Save and Close". Usually it will delete the selected line, but if it doesn't, I can just revert and try again, rather than try to figure out which line was erroneously deleted.

I hope an investigation is open soon, as this is beyond ridiculous.