Brady was never listed on the injury report with any sort of head injury, so he either never told anyone or the Patriots covered it up. My guess would be it was the former more than the latter. With that in mind, we don't know when or how this happened, but it really didn't seem to affect Brady's play all that much.
Bundchen also said Brady has had concussions in the past. But again, if this is true, none of them were documented. We may never know how many he's had or when they occurred.
While Gisele has no real reason to lie about this, she has openly stated she wants Brady to retire. Could this have been a ploy to push him in that direction? I doubt it, but that question is going to be raised.
I'm sure the NFL will look into this now, though, because it has to do with the Patriots. Hopefully they don't wrongfully suspend Brady again...