See this works for the limpet to return one thing, then when it goes back down for more it crashes into the planet or something. Goes down, starts blinking for about 1 second, then dies. Had that happen?
This can (rarely) happen, but it's due to one specific piece of material which is positioned in a particularly bad way and makes the limpet crash. You can recognize it by launching multiple limpets at the same time: one of them will die every round trip, as it selects the "bad piece" to collect. So if e.g. you launch 4 limpets, 3 will return and one dies, then 2 return and one dies etc. until all limpets die.
Best way of dealing with this is to launch at least 4-6 limpets and then "replenish" the one which dies every time you get the expiration message. Granted, after you finish collecting all the materials, you will have to waste all surviving limpets, but it's not like they're expensive. Just fill your cargo with them and go to town.