I have the same issue. Are there other boxes to search than these three in this house?

Anybody found a fix for this?

the trigger for the third crate is on the other side the only way I was able to get to it was using advanced vault mod.

@jojobina is right. The trigger is behind the crate. What worked for me is to aim between the crate and the back wall then pressing "V" to step over. This allowed me clip a little bit closer to the trigger and mark the crate. You just have to be quick when the icon appears as the collision detection will push you back out.