Sometimes items will be rendered in pneumatic tubes after the items have already past and even left the system of tubes.
They are rendered as unmoving staying in one place.
Breaking the tube and replacing it solves it. Also waiting for a time clears up the items rendered in the tube.

I've only been able to reproduce it after I reloaded a word which had items running through the tubes, and with magtubes. Is this for you the same, or does this happen randomly as well while the world has been running for a while?

The world had been loaded for several hours. Then I set up the flax farm in the picture with seeds and string being pumped into the tubes at irregular times over the period of several hours. This bug happens with regular pneumatic tubes at random times.
I've used the watering can from Extra Utilities to make a large number of seeds and string go through the tubes in a short time. This did not cause the render bug.
As far as I can tell it is random when the bug happens.
I'll let the world run again today and see if it takes long for the bug to reoccur.