I am a bit confused here.
If my fleet save returns with n million, minerals for example, and I reduce that by 1 million to keep 1 million on my planet.
I send my fleet save back into space. Maths tells me I should have 1 million minerals, for example, on my planet, plus what has been produced.
Why do I only have 999nnn on my planet?
What happened to the rest?
Did it go into space?
Was it stolen by space hamsters?
It must go somewhere. Looking like a bug to me.

Most likely. It's called “corruption” and it activates when your storages cannot fit all the resources on a planet. Which is likely to happen when a big cargo is unloaded on a planet after your fleetsave returns. Corruption rates can be found in storage infos, e.g. Metal Storage.

Production of a resource stops if the corresponding storage is full. And corruption is applied as a negative production, decreasing your resources in real time. So in the seconds between loading resources into fleet and actually sending it you will lose some resources. For example, if your total was 12345678, you edited it to 11345678 to leave 1M on planet, but before you sent the fleet 678 was lost to corruption. Your fleet will still take 11345678, not from 12345678 but from 12345000 that was actually present, leaving only 999334 on the planet.

If you believe that storage space wasn't a problem, please, provide more info about your situation.