I used to notice a problem with that, it was prominently when I had the B button pressed down and when to press the A button. The side of the A button would catch and you'd have to press hard to make it click in.
Like a lot of people have said, a simple silicone grease treatment helps with the stock d-pad and button issues.
I eventually found that the A button stopped doing this, I think it was a combination of using the grease, and also just general wear on the button.
Long term, you're much better off getting replacement buttons like the 3D printed ones, and installing those.