So the bug tracker is taking a bit to get up due to some DNS issues with the host, but it'll be resolve (i hope) shortly. Until then, feel free to post below!
Many bugs have already been fixed (operatives stuck on cancelled missions, location not updating in active mission menu, etc),
some are just incomplete features (plot/challenge failure is currently being built and will be done soon, and the only real way to fail currently is if the object you're after isn't there anymore),
and some aren't actually bugs, but dependent on other features to work "properly" (namely: the notification system to report why certain things are happening).
Post your bugs, with:
How you got that to happen
What you expected to happen
If you're able to make it happen again