I noticed something else... The bug is similar to the above one...
Have identical 10 items in base 1 and identical 20 on base 2. For my test case this item was antimatter. However I think I have encountered this on every item I have tested it...
Now transfer 10 items in base 1 to base 3. Hit transfer and they are on their way... So far so good.
Now go to base 2 and try to transfer that 20 items... Whats this? The up arrow (the arrow to send) is disabled? Also notice that the down arrow is enabled!
I think I know why... Try clicking the down arrow only once. The up arrow is enabled allowing you to transfer one and only one item (since you reduced it by one). Okay now hit the down arrow till it is disable. Even though you haven't sent anything yet, you can reduce what you are sending... Okay now since it's disabled try increasing the send. As you can see your up arrow is now disabled with 10 items left in your base and 10 ready to be transfered.
What I think happens is the index data of the previous transfer overrides the current one you are working on...