I am having to frequently check LTN manager for trains in NA state to tell them to finish loading. It's always on the loading side, if that matters. I'm still numbering my stations, so the route isn't lost when the temp stations are removed/train switched to manual.

Here's a save file with my wood pickup broken.
https://www.dropbox.com/s/adhha7oa60vqbf2/Krasatorio2temp.zip?dl=0

Here's a slightly later save file where my raw rare metal pickup broke. The error happened sometime in the 10 minutes between savefile 1 and 2.
https://www.dropbox.com/s/m0tn4l8jrcbhvb5/Krasatorio2temp2.zip?dl=0

I checked the LTN debug log, no messages of note in there.

Here's an even better save - the train heading to red circuits will lose its temp stations upon arrival.
https://www.dropbox.com/s/5rea4gu58ctrx2j/Temp%20defect.zip?dl=0.

I'm having the exactly same problem and it's just happens with the same one train every time.

Hi, i have a similar issue, my trains go to the first (temp) station and then go back to depot without even loading. And it loop again and again. I disable this mod for the moment. I hope there will be an update cause this if a very good one for me.

Yup. LTN is adding temporary stations before the target station. Temporary Stations is interpreting this as a user temporary station and being naughty. The two authors need to get together and work out an interface.

The "switched to manual" that the OP noted is entirely dependent on the in-game settings for Temporary Stations. Those that don't have the "manual" checkbox checked will see the train circle around between depot and the target pickup.