Over the years, many developers have chosen to dive in and make vastly complicated build systems out of SCons, which sometimes don't work quite as expected. As a general rule, make sure you need to reach for a complex solution before you do so. SCons is mature software and has evolved over time to meet a lot of feature requests, so there is often an easier way to do something if you can just find it. The SCons community can be helpful here - the discussion lists and chat channels can be a way to find out if something can be done an easier way before embarking on an implementation.
When something does misbehave, trying to isolate the problem to a simple test case can really help. The work to create a reproducer often helps you spot the issue yourself, and a simple example is much easier for others to look over and possibly spot logical flaws, misuse of the API, or other ways something could have been done. In addition, if it turns out there's actually a real SCons bug (we believe it's a high quality piece of software, but all software has some bugs), it's very likely the bug filing will result in a request for a simple reproducer anyway.