The syndicate fan site here [url=]http://syndicate.lubie.org/[/url] has some helpful information for the series (walkthrough, maps etc)

When you playing on Orbital Station there may occur random glitch when your active agent is 1 and you reloading too many times, after few pickups or immediately on the beginning you can't pick up any new items or when explosives are dropped in corners. This will happen in DOSBox and Windows port, no exceptions. To prevent this make sure you select agent 4 or 3 when picking explosives. Also when you playing in DOSBox in no-buildings mode (makes run that level faster) your agents will have faster reactions and regenerate but unfortunatelly explosives will time out faster so it's harder to kill and pick up last explosive behind the time gate with mere seconds unless you lure epoch agent closer.

Bug officially confirmed on:
https://groups.google.com/d/msg/syndicate-wars-port/oSitcZkFcSs/h1R5wVi9xKEJ

On the Moon level you don't need kill these two lone scientist, murder all seven near the Ion Gate first because if they are kept alive after nine minutes if any of them touches Ion Gate mission will fail. If you killed them, after nine minutes cutscene showing Ion Gate will trigger but since no scientist can activate it you can still finish the mission and kill these last two remaining scientists. Note that your mission is only kill them, you don't need evacuate like in PSX version. To survive initial attack group agents, switch weapons to plasma lances and one agent to stasis field, max red mist drug for all agents then run into tight corridor below you and activate stasis field suspending epoch agents, run to end of corridor and eliminate all spiders.

Well it's not a glitch but how game triggers mission fail when screen is darkened on Colombo: when you lose any agent also have Chromotap and Displacerton in Research hit R when screen is darkening, you will meet with clean debriefing and put to Ops panel. Now you can use researched items on REF20 missions. Displacerton is especially useful on Moon mission if at least one agent have it equiped.