The scale of Antman compared to the electronics he's destroying, and the size of the seam he's going through, doesn't make 100% sense, but logically, it does make sense based on what we are told.
While Scott says
I have to shrink between the Molecules to get in there, it's a layman's comment though instead of a 100% technically scientifically accurate phrase. He's figurative, not literal, at the time. He's not actually the size of a molecule when he goes through, but he does get that small eventually.
Scott breaks the shrinking regulator, allowing him to go smaller than it's default setting. He continues to shrink enough that he can get in the Yellowjacket suit's electronics, and starts destroying stuff. But he is still shrinking. He does as much damage as he can while he continues to shrink to subatomic levels. It's not an instant shrink. And Scott still has his normal human level strength, so he can destroy the electronics without a problem.
Edit: Yes, there are issues with the visualization. He goes through the middle of the cap on YJ's suit, not at a seam. He looks like he disappears at that size, but then looks big compared to the electronics inside. These are production errors. Notice this picture.
Those things marked 457 likely represent a SMD resistor. 1, they are marked wrongly, as SMD resistors are marked on the long size, so the number is oriented wrong. 2, they are sitting on top of multiple traces. It's obvious someone who's not an engineer created this visual effect. The smallest resistor with text on it is a 0603 resistor, which is 0.06" x 0.03" (1.6mm x 0.8mm). Roughly the size of a common flea.