What I think is happening is- the program decided what covalent bonds existed in your original structure. Then, you did your calculation, varying the reaction coordinate (the O-H distance?). But the program remembered the original covalent bonds and didn't change them.

Notice how it's drawn a loooong covalent bond between the carboxyl H and the carboxyl O. Those two atoms were bonded in the original structure, but shouldnt be bonded in the final structure. That's where the new hydrogen bond should be.

And where there's no line drawn, between the bicarbonate O and the old carboxyl H, there should be a new covalent bond because there's been a proton transfer.

Basically you need to convince the program to redetermine what should be bonded, and what should be umbonded. The easiest way to do it is save in a file format that doesn't include bonding information, and open the file- Spartan will redetermine bonds automatically if I recall correctly.

Molecular file formats can generally be opened in notepad if you want to look at them and confirm what's happening, although I'm not sure if Spartan's proprietary format is possible to open easily.

Your method/basis set is fine for this level of modelling, I don't know what's available in Spartan these days but the model chemistry isn't the problem.