I think ultimately this comes down to two or more officials in the crew that called TAMU, ISU and Texas displaying (whether consciously or not) some very significant bias against Nebraska. There are probably others, but it's not as obvious. The stats point to this. I don't think it has to do with Bo. Not that his behavior is helping, but the issue with Nebraska leaving the Big 12 (which almost led to the end of the conference) is much bigger than Bo's anger.
Officials' futures were at stake during this whole off-season fiasco, and don't think for a second that officials are above this type of bias.
If you look at judgment calls and penalties with significant gray areas (mainly holding), these are going against Nebraska and in favor of their opponents too consistently this season to be by mere chance. Refs are supposed to be pillars of objectivity, but
even the best can fall well short of this.