This forum thread over at the Steam forums has a comment by a user with the username suchotek having a similar problem to you, having only a handful of modifications installed but receiving an error indicating more than 50.
This person fixed the issue by removing the following registry key;
As always, remember to backup your registry before making any changes.
This forum thread also has a couple of suggestions to prevent this from happening in the future;
- To have a mod installed you don't have to be subscribed to it, unsubscribe to mods that are stable and you don't think will receive further updates, then you can subscribe to more
- The 50 mod limit is specific to Steam Worksop, mods installed in Nexus do not count towards this limit
It is mentioned that this issue is a bug, but I don't have anything beyond a forum post to cite so this is possibly untrue, and this could have how Valve intended this to work. For more discussion in relation to this issue check out this long thread, also on the Steam forums.