No worries!
If you choose a different choice, you should always get a chunk of new text adapted to that choice.
There are probably a few lines of text that are duplicated in both routes, which might look like skip isn't working correctly, but for the most part the branching script should be unique to each route.
I'm not sure if you are referring to those small bits of duplicate text, or are encountering larger chunks of unskippable common text, which would be a bug. It might be useful if you can give me some examples of where this happens.