I recommend going through the Corporate Security Handbook (old SR2 book if you can get your hands on a copy) for ideas, but here's a few:
- Ruthenium Polymers don't make you invisible IIRC, they kind of make you look like a cloaked Predator (from AVP movies, or the Predator movies). Standing still or moving slowly are hard to spot, but a fast moving person is more noticeable, reduce the runner's bonus if they're moving fast.
- Like Kid said, bullet holes and blood splatter or blood dripping down the body from a wound (again think of the neon green blood from the AVP/Predator movies when the predator got wounded) will stick out in dull gray corporate areas
- Also remember that the suit runs on batteries, which can run out. Also, the electrical system can be shorted if the runner takes any kind of electrical damage (same goes for cyberware as well). When in doubt, the enemy mage has a lightning bolt or lightning ball spell. Let the players know who's boss

- Security cameras: adding low-light/thermo is relatively inexpensive for a corporation
- Guard animals can smell very well.
- Spirits can see everything just about, ruthenium doesn't hide astral signatures
- Same goes for mages who can astrally perceive/project.
Mobile Base ideas:
- They need to stop for gas sooner or later, transactions can be traced and then compared to video footage (the whole 'plex has cameras everywhere besides the barrens, they'll show up sooner or later and people can be actively watching certain areas for an RV).
- Astral signatures - a person leave an astral trail that can last for several hours. The more intense emotions (i.e. anger/fear from a gun fight) the longer the signature lasts. A mage can assense the signature and then follow the trail through the astral plane.
Just remember, if there's a way to do something with tech there's always a way to undo it. At the same time there's always another way to do it
and undo it with magic. Damn, talking about all this makes me want to run a game again!