Vanilla, live branch, breath of fresh air update.
This issue is mouse input related and can take effect when paused or unpaused, the delay/lag is random but does not affect/is not affected by keyboard inputs/hotkeys (or atleast if it is affecting the keyboard, it is minimal to the effect that is unnoticeable meaning if you use keyboard inputs, this issue isn't noticeable)
Currently using the mouse to do anything seems to have a delay/lag when clicking something, the problem seems to cause the game to lag for a few miliseconds to a few seconds (Literally causing everything on screen to stop for said duration), then the game seems to register that you wanted to click something, however instead of registering the previously clicked icon the game instead checks where where your mouse currently is.
Everything from clicking top bars (research, starmap, vitals etc), overlays (power, piping,automation etc), anything on the map (buildings, gases, materials etc), placing buildings (pushing/holding the mouse click to lay down buildings, pipes, wires, etc), on building priorities (1-9 priority of a building).
There are times when you click something and it makes a sound that you clicked it, but doesn't do anything, not even click the part of the map your hovering over (this is noticeable when changing priorities of a building)
An example is you click to build something like a tile (I believe it makes a sound which makes you think you have clicked it) then the game lags/stops for 1-2 seconds, in this time lag you have moved the mouse with the assumption that the building is being loaded so it can be placed it in a second, after your mouse has arrived at its location, the lag has ended (or during the lag even) but instead of loading the building to be built, it instead clicks the location on the map trying to reveal its information (if there is oxygen on the location, it will show the info for said oxygen,etc).
This is made more apparent that instead of holding it at the initial click location until the lag ends, when you click the initial location then the game lags, you move the mouse and remember this is bugged, then move the mouse back before the lag ends, then the mouse accepting the initial click since the mouse is back over its location.