I think I know what's happening. When you insert a page number using Word's Insert>Page Numbers..., the page number is inserted in a frame in the footer. A frame has text wrapping which would prevent an overlap with normal text. However, footnotes and endnotes
have an artificial positioning that makes them ignore the text wrap of the frame.
I believe at some time you may have manually adjusted the position of the page number frame, or you may have added page numbers and later revised your bottom margin, at which time the page number frame did not move down. This isn't showing in the body of
your document, because the frame wrapping stops normal text from overlapping.
In any case, you can fix this by opening the header & footer. Then you can either select the page number frame and drag it down a little, or you can select the page number field inside the frame and paste it into the footer so it is positioned inline with
the footer. If you choose the latter method, delete the frame and apply centering to the footer to place the page number back in the middle.