Personally, I haven't had many issues with subtitles on Crunchyroll, but there are a few issues I have had with Crunchyroll in general that are annoying.

1. Localization changes. This isn't specific to the app, but its really annoying when an anime localizer changes the dialogue to match their personal politics instead of just translating what the original anime creators intended whether the localizer agrees with it or not. In some cases this is understandable, such as when some pop culture or political joke is made that cannot be understood in a different culture, so swapping that out for a suitable replacement joke or reference is fine. But when entire lines are changed in a scene that drastically alter a character's personality or motives, that's a problem. This translation is sometimes also used as the subtitle text, which means sometimes subs are inaccurate because of a localizers personal politics. This has happened with many localizers in the past, but Crunchyroll seems to accumulate these bad changes more than others.

2. Some content is not available on one platform, but it is on a different platform even within the same region. For example, Bubblegum Crisis is not available on the Android TV app, but it is available on the Xbox Series X app, within the same home. I don't know if that is a bug or an oversight, but it is pretty annoying.