So let me explain what's going on here.

As long as the floor button in my map (see below) isn't pressed, "Autoportal A" will stay active.

When the button is pressed, Autoportal A turns off and is replaced by Autoportal B. This, however, is not my problem.

My problem is that once you step off the button, Autoportal B turns off, and Autoportal A emits a blue portal. Stepping on the button again will still turn off Autoportal A and turn on Autoportal B, and vice versa, but no matter how many times you step on it, Autoportal A will still emit a Blue Portal.

This can result in this.

Therefore breaking the entire puzzle.

Note: Shooting a portal before stepping on the button precludes this from happening.

I remember I had a problem somewhat like this a while ago when messing around with autoportals; sometimes there would be 2 blue portals and 2 orange portals, sometimes there could be two sets of portals out (similar to how the cooperative campaign works.) Do you have outputs that, when the button is stepped off of, disables autoportal B and enables autoportal A again? Then your solution is to make an incomprehensible delay for autoportal A to open after autoportal B is closed. I used 0.01, you can't notice it at all.

I've had this problem before too. You need to make sure that only one portal is active at a time, deactivating the old one first. I'd use a pair of logic_relays that CancelPending each other to make sure quickly pressing/unpressing the button doesn't mix up the outputs.