hmmm. There's nothing special about the last bot that put something in so it should be all-or-nothing really. Can you do me a favour and send me your level please so I can have a look? If you could set it up ready to go wrong that would be great.
Here are some example test files which demonstrate this bug:
This is a large scale production of clay pots that I'm doing (with support bots leading the production chain... I'm doing clay pots to show it more clearly). Here you will see several workerbots making raw clay pots simultaneously, and when it hits the storage peak, all but one will stop. If I ramp up production of the clay pots after the storage containers are full, all of the bots but one are glitched out.
Another situation is here:
Here I have multiple bots both consuming and making raw clay pots. The production of raw clay posts is slightly higher, so one or more of the bots are going to glitch out but the others will continue afterward. A situation like this can have a second or third bot eventually glitch out. If you aren't closely paying attention to the situation, what will happen is that the glitched out item production will gradually start to fall until the storage containers eventually go empty.
I hope that helps you out in seeing a test condition to catch this bug.