If there was some Heavy or Special Ammo drops that did not get picked up earlier in a mission, strike, etc. then for whatever reason, it will not drop anymore in later sections. It can become quite frustrating to have two weapons effectively useless simply because they were full on ammo, in the areas where the ammo for them dropped. There may also be situations where their ammo was unobtainable wherever it dropped. I suggest despawning these ammo pickups after 5-10 minutes so that they continue spawning later on.
I have seen no evidence of this, and have left plenty of ammo on the ground going from area to area and it still continues to drop later on. I've done so with all three ammo types and not experienced the issue you seem to be having. Ammo drops are based on the RNG, so it's possible you're just not seeing a lot of ammo drops due to RNG. If you can somehow record a video of you working on fact finding for evidence of this being a bug, please do so and share the link to it.