The problem you are experiencing is most likely due to a PHP caching/optimization program installed in your server. For example, the APC (alternative PHP caching module) has some bugs that will cache an included file and they try to include it again (resulting in a PHP redefinition error, require_once error, etc). For details of the APC bug and possible solutions check out this link: https://pantheon.io/docs/alternative-php-cache/
There are caching modules from other vendors (eg: Zend) with some similar issues. So you may also wish to disable caching of SecAst files since they don’t create much load on a server (relatively static, low volume). This is not a SecAst bug, but future versions of SecAst will try to detect the caching software and work around the issue.