When using the loader, count your rounds as you put them in and make sure it matches what it shows on the mag. When I use my MagLula loader, sometimes (not often, but it does happen) it shows I have 10 rounds when I only have 9. I have personally caught it each time, so I don't know if that could cause a failure or not, but I have had it throw the count off somehow. I always just unloaded the mag and reloaded it and I have never had a problem.
If you are having problems with specific magazines, then take them apart and clean them. Also make sure there are no burrs on the follower or something wrong with them. You can number your magazines to keep track of the ones that have problems vs. the good ones.