It seems to be related to how close to the "hit box" (for lack of a better term) you are. I have had it happen more with larger dinos (brontos and wyverns, for example) when you try to access their inventory from their feet, or in the case of the bronto, also their platform saddle. Mounted, however, you can transfer all as normal. And with the wyvern, if you stand directly under it's belly and transfer and target the belly when you access the inventory, you can then transfer all.
I have also had issues transferring from the incubators if I wasn't close enough.
Wild Card, please fix. It is urgent. ARK is all about harvesting and transferring your bounty to and from dinos. This is a significant hinderance to work flow.