I wouldn't call this a bug in mIRC, but a fault in any auto-resume system being that there are too many scenerios to consider. You can however avoid this by grouping your downloads into subfolders by nickname... then you have less chance of receiving two different files of the same name from the same sender.
Presently, mIRC only has 4 options for its Auto-accept feature: Resume, Overwrite, Ask, Cancel. Perhaps Khaled could add more options like Rename, adding a (1) to the end of the file.
It could also default to Renaming if mIRC detects the resume file is a different filesize or from a different sender.. but then perhaps some people enjoy how it works today. *shrugs*