The other day I spotted a mature tree that features two of the most common pruning errors. The red arrow points to a branch stub. In this case, a limb was pruned off about 8 inches out from the branch collar. The branch collar appears where the limb connects to the trunk and is the natural location for a tree to grow over a pruning wound. In the photo you can see that the branch stub is rotting away, while the tree has developed an exaggerated branch collar in a attempt to seal over the wound. If this branch had been pruned correctly (at the branch collar), the tree would have sealed the wound by now. However, the rotting branch stub prevents proper wound healing and allows wood rotting fungi to penetrate into the heart of the trunk. Rule #1: don't leave branch stubs when pruning.
The yellow arrow points to a lower limb that has been pruned back at several points but still extends 10-12 feet from the trunk. This limb is now dead and starting to decay (note missing bark on limb near trunk). Hacking back a lower limb places the entire remaining portion in the shade of upper limbs. Pecan is shade intolerant; so if a limb does not received enough sunlight, the tree aborts the limb. The best course of action is to remove lower limbs completely, pruning the limb all the way back to the trunk and just outside the branch collar. If not pruned off, the limb shown in the photo above will probably end up being shaken off during harvest (just hope it doesn't break something when it falls). Rule #2: prune lower limbs back to the point they are attached to another limb or the trunk.