Slitherine

I'm playing the Stalingrad scenario as part of the 1939 campaign (at general difficulty level). There are supposed to be only 2 sea transports available. However, I was able to embark a 3rd unit. Now sea transports show as -1/2. I have a save file if needed.

That is a very interesting bug you found there. No need for a save file, I was able to recreate it.

Here's the hiccup:

If you have a port that is also connected to rail, you get the option to choose NAVAL or RAIL transport, assuming you have both still available.
If you have reached either your maximum NAVAL or RAIL capacity, the game attempts to default to the type of transport you still have available. (Notice you did not receive a pop up asking which type of transport you wish to board?)
The default transport for a window not popping up, however, is set only to NAVAL.

So if you have RAIL transport left over, you can generate infinite NAVAL transports at any port that is also connected to a RAIL line. However you cannot generate this problem of infinite NAVAL transports is you attempt to embark on a port that does not have a RAIL connection (embark is greyed out).

Exactly right. I was initially in Sebastopol when I launched my 3rd transport. When I tried it on another port (no rail as you said) it didn't let me. I only found it by accident, not realizing that I still had two transports at sea before I tried to launch the 3rd. A really minor issue. The game has been rock solid for me. I can't wait for the expansions!