In order to answer this question, we need to remember that the science portrayed in Ant-Man isn't just wrong in the real world, it's also highly inconsistent within the film itself.
However, the situation you are describing (when The Wasp shrinks down further than is safe in order to disarm the missile) is very similar to a situation we see at the end of the film, which has Scott Lang shrinking down to smaller than is safe in order to shut down the Yellowjacket costume. The description given by the characters is that they have to "slip between the molecules".
When we see this happen in the final battle between Scott Lang and Darren Cross, we watch as Scott starts getting smaller and shrinks at a seemingly continuous rate, entering the control panel(?) on the Yellowjacket suit and destroying parts of it as he shrinks. We can assume that the same thing happened to The Wasp when she shrunk to disarm the missile, continuously getting smaller (and breaking parts of the missiles control system while she shrunk) until she entered the Quantum Realm.
However, when Scott enters the control panel(?) of the Yellowjacket suit, he is still visibly larger than the various electronics that he starts to destroy as he shrinks, and as such cannot have been small enough to slip between molecules to enter it in the first place. A possible explanation for this is that his decreased size meant that he could put more pressure onto the control panel(?) casing (thanks to the fact he keeps the same strength while shrinking), breaking what was once simply too hard for him to break through as he shrunk. By that point, his shrinking was out of control and he began to enter the Quantum Realm.
In short, The Wasp was able to destroy the electronics inside the missile as she shrunk, completing her task before she became so small that she entered the Quantum Realm.
As far as I am aware, the exact event of The Wasp disarming a missile and getting lost in the Quantum Realm isn't taken from the comics.