Hello Maria, are you really sure its an issue of the track matte? The thing is - I never experienced any problems with it, and based on the supported features list, there shouldn't be any.
What else might be the case - its the way how shapes are grouped in the shape layers. Be aware:
1. If you converted .ai files to shapes, chances are high that inner structure of shapes group must be cleaned up.
2. If your shape layers has merge paths inside - it will fail too. Workarounds should be used to avoid this.
If none of the above valid, make sure no other non-supported feature is not used. Alpha Track Mattes shouldn't cause issues. Let us know how it turns out!