What type of subtitles are you using? If you look at the information in the wiki documentation (https://wiki.videolan.org/Documentation:Subtitles/), it might help clarify why you are having this issue.
Could you give us some more information about the software version and setup you are using? Also, does this problem occur with multiple videos or just a particular one?
Have you looked at the Developer section of the VLC wiki ( https://wiki.videolan.org/Developers_Corner/ )?
It looks like "Get Started at coding on VLC" and the "Hacker's Guide" would offer some useful starting points.