Mike & Nacho discuss the assassination of Tuco. When the cafe/restaurant is in shot, the cloud formations change.
At 41:18 -while both Mike and Nacho had previously agreed on a $50,000 payment Nacho pays only $25,000.
When Mike calls 911 on a payphone, he inserts money. This is unnecessary, as real payphones make 911 calls free of charge.
When Mike tosses the envelope of money on the table, you can see that the serial numbers of several bills are identical (SGI8017583Q), Benjamin Franklin doesn't quite look right, and clearly shows "For Motion Picture Use Only".