How come the plecos aren't taking care of the little spots of brown algae?

They getting theirs elsewhere, I guess. Otocinclus go after the diatoms better than any other fish.

It's a common misperception that plecos will rid a tank of algae. Pleco's eat different types of algae on an individual (per fish)basis. Most will ignore brown (diatom) alage. I've kept plecos for a long time, and honestly, I really don't know what they prefer. I keep plecos more for the sake of keeping plecostomus catfish than for their ability to eat algae.

Otocinclus catfish are best for brown (diatom) algae. Siamese algae eaters are best for black beard algae (or red algae). Rosy barbs and Flying foxes are great for green hair algae, and Amano shrimp are great for detailing your tank (all but diatom, cyanobacteria, and green spot algae).

Low-light conditions, for one.

What about the green spots on the glass that are almost impossible to scrub off? Is that diatomaceous too? The rhino pleco I have will do a little damage to it but not much...