Are you targeting the fragments when you launch a limpet? Because if you do, it will only collect that fragment and then immediately expire. If you don't target a fragment, the limpet will collect everything in range for a set period of time (up to 12 minutes with the 3A collector module).
Also, if you're moving, the limpets will crash into your ship as they attempt to drop off the fragments at your cargo hatch - they take damage and eventually just die (you can hear them scrape against your hull). So you need to just sit there while your limpets do their thing. To speed things up, you can install more than one limpet controller, allowing you to launch more limpet drones simultaneously.
I have very few problems using the collector limpets - they actually make mining fun.