This is a list with issues in the SP portion of the game. If you have an issue that's not reported here, please post about it in the HW2 Bug Report forum.
1. If you skip through the opening movie and opening cut scenes by rapidly hitting escape, you will leave the door on the mothership open. To workaround, don't immediately skip through the opening NIS (non interactive sequence), instead, wait until you see the collectors start moving the core. - Fixed in 1.1
2. If you build a second collector at the end of the mission, and queue up a third (and leave both docked), then they will not show up in Mission 2, and you will have lost the RU. Workaround, build the collectors in M02. - Not Fixed in 1.1
3. The Research module appears and disapears from the motheship as the opening intro NIS plays. - Not Fixed in 1.1