In principle there is nothing wrong with how Paperpile handles APA style. I assume for most your papers you will get the correct initials as expected.
However, there is one caveat. If you have for example two papers from the same author and in one paper you have saved the author as "John Doe" and in the other case only as "J. Doe" Paperpile thinks these are two authors and according to APA style tries to disambiguate by adding the full first name. The solution is to make the author names always consistent.
At least this was the solution for some other users who ran into this issue.