It's the settings and perhaps you are not reformatting after each download.
I think if you have the camera to start numbering anew with each card, it will start a new folder for your images each time you change a card and start the sequence at 0001. If the card hasn't been reformatted after downloading, it may start a new folder and rest the file numbers.
I have all my Nikons set to not reset the frame count with each card. Once the count gets to 9999, it will start a new folder. The other situation it starts new folders is if I switch the card to a different camera. Whatever frame number the second camera is on will be the frame number in the new folder.
Best bet is to get out the manual and set the camera to simply keep the file sequence going which it will until 9999 then it starts a new folder automatically after each 10,000 images.
However, I seldom look at my card once they are put in the card reader. Photo Mechanic (and I think both Bridge and Lightroom), handles dupe names and multiple folders without me looking and simply ingest them into my computer to the destination of my choise. If there are duplicate file names, Photo Mechanic will arbitrate the situation and simply append the file name with "A", "B", etc., however the preferences are set. I don't have to worry about overwriting.
Once my photos are downloaded, renamed and backed-up, I always will take the card and reformat it in the camera. Doing the reformatting in the camera makes sure that there will not be any issues with overwrites, corruption, etc. I never simply erase files one-by-one since that seems to haunt one later with card problems.