I had the same experience too. Seemed to be about 20 or so minutes into the movie and lasted a few minutes. It gave me a headache for that short period and I was getting worried until the next scene it went away thankfully. I seen the same thing in an underwater scene in Journey 2 when they r going inside the Nautilous.
I've now seen two different discs (I returned my Wal-Mart copy as defective and bought another at Best Buy just to be safe) - and I can now confirm that it happened on both. This was the standard 3D version, not the collector package.
During the affected part of the movie, it appears that the 3D depth setting jumps to a way higher value than the rest of the film. It's similar to cranking the depth slider all the way up on a Nintendo 3DS, on a game that already runs deep. The result is pretty much instant eyestrain and, if you're prone to it, a headache. Feels kinda like someone is holding a magnifier over one of your eyes.LIGHT SPOILERS in the timing description below!]
* The problem starts at exactly 11:15
in, and it's directly on a cut: the scene is just after Gipsy Danger does the overhand double-smash (aka the "James T. Kirk") on Knifehead. The kaiju goes underwater, then - on the cut - just as he comes up and bites Gipsy's arm, the depth problem appears.
* It lasts until 14:35.
The plasma cannon discharges, followed by a scene of Marshall Pentecost in the command center - he's walking away worriedly. Cross-fade to a snowy beach, as two small figures walk. Right when we cut to the medium shot of the old man and the kid walking the beach with the metal detector, the depth problem vanishes. It doesn't return for the rest of the film.
I would imagine that if a whole batch (or eight) of Pacific Rim discs exhibit this problem, it would be grounds for a replacement program. This really kills one of the movie's best fight scenes, though at least the duration is pretty short. Now that we've got the exact timing of the issue, please have another look at your own disc and post your findings here...