In the past, I have used spreadsheets and database programs (MS Access) for issue/bug tracking in simulations. This does require a way to identify the software build that correlates with the issue, so using SVN or GIT is a good way to accomplish this. The database/spreadsheet also allows me to collect ideas or suggestions from group members such as "I think we need to ad this new feature" or "I suspect there is a problem that should be investigated further", etc. This gives me a place to record the issue and it's resolution, even when it doesn't effect the code.
Note that I support new product development, so when we conduct a simulation analysis that will be used to predict product performance, we track the version of the simulation that was used in the analysis. If a bug is discovered, we need to be able to do "forensic analysis" to determine how it influenced the product decision process, so our procedures are designed to provide this ability.