Just out of curiosity, but why would you want to take a photo by hand when the INDI system is made for automatic workflows? I would almost assume it could throw that off (ofcourse would be nice if it didn't).
If you take one manually, then delete it manually before you proceed! I guess there could be a button to discard last picture, but again if you took it manually, you can also delete it manually as well.
Mainly, it is unintentional. But could also be intentional .
For example, pressing on the touch screen (Canon 650D) while adjusting focus. Or you want to record a video of the moon or Saturn, and forgot to set the dial or so.
Or maybe intentional, for example: I am at the camera, and not at the laptop, and the moon or Saturn is in the field of view, and you just want to snap the picture and not go inside to the laptop, ...etc.
Regardless, this action (intentional or not) throws INDI out of sync, and causes serious issues, as I described with plate solving and syncing to the wrong part of the sky.
There is no way for INDI to know if you have done this. The only solution is to implement a "download and discard" property in INDI that you need to explicitly trigger (i.e. press some button). But then again, why not delete from the camera directly?
I can't test this right now, but here it is from memory, so I could be off ...
Manual exposures while connected to INDI mess up the sequence. I see the frame count on the camera's screen blinking continuously, and the camera refuses to power down when the power switch is turned off. It will display 'saving image' until the battery is pulled out.
I will try to test again on the next clear night in a week or so.