Generally expect this application to be unstable. This is not a finished application and in no way stable software. If it crashes, don't panic. Please try to reproduce the problem and report the bug to me either by email or post it in the forums at the sourceforge project page.
On IGS only 19x19 games are supported. Any other size currently simply won't work. This is on my TODO list for one of the next releases.
When opening a board on Windows, sometimes there are display artifacts. Once the window got a bit resized or moved, the artifacts are gone. Another good idea is to enable "Autohide starter" in the preferences, this seems to solve the issue as well. This does not happen on Linux. I don't know the reason for this yet.
If you run a GNU Go score estimation and kill the gnugo process via task manager or killall, glGo will crash.
The SGF parser has trouble with Kogos Joseki dictionary. I remember this problem from gGo/Java, Kogo has some wired variations and is not SGF conform. This is on my TODO list.
When reading an english komi value (like 6.5) with a german locale, the komi will be detected as invalid (it wants 6,5). I did not find a solution for this yet. Switch to english if you are german and this bothers you, otherwise just ignore it.
The captures algorithm has trouble with Kos. When loading SGF files this could produce some wired results. With observed IGS games it should be ok as then glGo won't calculate captures itself but instead use the provided list sent from IGS.
On Linux, toggling the toolbar creates some artifacts; resize the window manually a little to fix this. I don't know why this happens, it's ok on Windows.
The fonts are not yet optimal, the underlaying grid disturbs the display. This is on my TODO list.
The new OpenGL scissor test causes problems with the cursor ghost stone in own games.
Automatch does not display a dialog yet. On TODO list.
The localhost server mechanism on Windows is a potential security risk if you run Windows without firewall. However, if you do such, you have much more serious things to worry about than someone hacking your Go client.
If you encounter trouble, please don't hesitate to tell me about it. What I don't know I cannot solve.