My diggles are always carrying stuff like logs, live hamsters or raw shroom caps, but not for building/producing. They just have them and refuse to throw them out by themselves into the Store. Anything i can do besides discarding everything on the gorund every once in a while?

Those objects are what they pick up to carry somewhere but then have that job canceled, either by you telling them to do something else, being attacked, or saving and reloading, in which case they may forget what they were doing. Normally shouldn't, but sometimes it may also happen if they go off duty mid-job.
So what you can do is be really careful to not command one who's carrying something, and do your best to avoid saving at such a time.