Well if you have same name file or similar time code , this can happen you could fill in the reel number to differentiate the files , it often fixes this type of issue.
Since AVID original goal was to off line and generate an EDL maybe you could use this path to DaVinci resolve then via fcpxml to the wonderfull FCPX NLE then back to AVID using EDL X … which can convert fcpxml to EDL CMX 3600 which AVID loves.