Following checklist should be completed in order to completely remove the all the dependency before exporting the solution and importing to your target environment.

1. Make sure all relationships are removed ( i.e navigation from left hand side on form editor)
2. Any Lookup field from that custom entity is removed
3. The most important and neglected one and for which I find people scratching their heads is when this lookup is removed from the form and even entity is deleted. Still  Get dependency error something like below:
   Resolution:  The lookup field was being referenced on another lookup which was acting as a “Dependent Lookup”. hence this entity was showing as system form dependency.  So i went to other lookup field —> changed properties and unchecked the option “Show related records”.You can also try to remove that field –> Publish —> add again —-publish.

Hope this helps!