Is there a given percentage of unwanted species that people usually find when stocking? I know it depends on the place you get your fish from but didn't know if I should expect a certain amount no matter what.
Simple question long answer.
It is a definite risk depending on what species you order. You basically answered your question when you said "....it depends on the place you get your fish from...". Some fish farms provide a lot purer lots of fish than others. Generally expect a higher percent of unwanted species from traveling fish trucks and "jobbers". Smaller fish farms who raise their own sunfish species are IMO more likely to have contaminated fingerlings due to lower quality control of the systems - maybe not. Also the more species a fish farms deals with the more possibility there is for contamination. Their source of fish plays a big role. Many farms buy all of a certain species such as RES, CC, grass carp, HSB. Basically if you are really concerned, I think you should do your homework and ask feedback from several of their customers. Any reputable fish farm should be willing to give you a few names of their
regular customers.
IMO most of those that can or do sort fish from the fish farm are capable of only sorting the FHM to make sure there are no obvious fingerling sport or trash fish in the lot. With a pure specie of sunfish it becomes quite difficult and for most it really does not matter all that much unless you have a very specific goal in mind. Most pondowners by far just trust the delivery trucker. Since I have lots of experience (academic and personal) identifying at fish, I never fully trust the source especially when the stocking is important to me, personal stocking for someone, or my reputation.
From my long time experience with training and experience in fish taxonomy (identification) it is pretty hard to speciate small 1"-3" sunfish which all look very similar as you correctly noted above. For other species such as CC, LMB, SMB, YP, and crappie it is not real difficult to sort fingerlings. As you probably know as the pure specie of sunish grow closer to maturity they become easier to recognize. The other difficult part of this topic is fish will change intensity of body colors due to several factors. This makes identification quite difficult especially when dealing with large numbers of stocker fish (100-500).
Depending on how many fish you are getting, the size of the pond, and the specific goals for the pond, your better plan would be to casually go through the stocker fish (FHM) to make sure there are no obvious unwanteds such as greensunfish, carp, goldfish, bullheads, wrong type of bass, crappie, warmouth, sticklebacks, or species you did not order. At the fish farm fish can easily jump, get dropped, or someway get mistakenly mixed in with a batch of fish in an adjacent hauling tank on the truck or even get misplaced into a rearing pond.