Those plugins and add-ones tend to sometime do things that otherwise you wouldn't do if you were using the native (CLI?) client.
For example, if you were working with an Eclipse + ClearCase plugin, any change in a file, even adding a new line, will initiate a check-out operation (depending on the configuration).
Specifically for Git, you should be aware of its internals to properly work with it. Using the IDE hides those things from you. In normal trivial operations, it will work. But, when you are facing a source control issue (ugly merge, cherry-picking, rebase conflicts) you will have to go to the CLI to resolve, but then you have no idea what were the actual commands that the IDE ran that got you to this situation in the first place (plus you have no experience with the CLI at that point).
