I noticed that sometimes WGBS/RRBS experiments have what I call "incomplete" methylation (there is probably a better term for it).
Here is an example (generated by MethylKit):
Notice how the unmethylated side of the graph is okay, but the methylated side drops off at the end. The last bin should be highest, but it's not. The rest of the metrics seem okay as far as I can tell. Is that a problem? Is there an explanation?