Yes, that is the problem I am facing. But it also comes up when I don't start with = in the first place instead of deleting it as in your case.
Another issue, I noticed today is
I copied a calculator result. Returned back to Aflred after a minute and pasted it, so as to do further calculations. The result had "," included which is good and I know there are settings in Alfred regarding this. However, it is not eligible for calculation anymore, it goes to fall back searches.
e.g.
=56+45,667
(45667 was what I had copied earlier and then pasted back)
I think it would also be better if thousand separators are shown when typing numbers as they are shown in results or when pasting results.