The "guns have been laid" by the mainstream media as far as the Minutemen are concerned. One incident, no matter how minor, is going to get amplified all out of proportion. I hope the Minutemen are vetting supervising their volunteers very carefully.
The one sure way for them to look bad is to have some open-border sympathizer to penetrate the group and then rough-up an illegal. The other way that I can see to sabotage the Minutemen would be from the Mexican side of the border: send over a bunch of thugs to deliberately attack a small party of Minutemen with the idea of getting them to pull their weapons.
If the Minutemen become too large a thorn to the administration, they'll be turned into a Waco puddle. Probably using some kind weapons baloney as the excuse.