Sure. This is... For better or worse... Somewhat natural.
The state of the Site
Skeptics is in a crucially-important stage of its lifecycle: influx of new users, establishment of community-norms (what is on-topic here, what should a good answer look like, how should we deal with poor-quality content), and plenty of arguments over how to deal with users and content that don't meet those norms, and personality clashes, and LIONS AND TIGERS AND BEARS!
...aaand there's the chicken-and-egg problem of the site needing moderators to keep matters from spiraling out of control, while at the same time not having enough of an established community yet to actually elect moderators.
So we picked a few volunteers, to moderate until the elections happen. And they're doing a bang-up job of it. This is mostly "janitorial" work: dirty, thankless, and never-ending. Oh, and they're pretty much guaranteed to step on toes left and right, simply because they can't sit idly by and watch when conflict arises.
Name-calling, baseless accusations, flame-wars... That's what they're here to put a stop to. Whether the target is another user or another moderator, their instructions are to nip it in the bud.
That said... It sucks when you see a comment just disappear, with no indication as to why. Makes you kinda paranoid about it. Especially on a site where the idea of just taking an explanation at face-value is... A bit contrary to the fundamental objective. And yet, you're gonna have to see a lot of that, for the reasons I've noted above.
So what can you do?
Moderators need feedback. Actually, everyone needs feedback, whether they're new and asking their first question on the site, or experienced and trying to deal with a troublesome situation. The last thing we need is apathy. The comments you leave, the votes you cast, and the discussions you raise are critical to making this site a success.
But be tactful. There's no value in calling out another user for something you can't prove. If you see something that makes you uneasy then ask about it, here, on Meta. Be thorough: describe what you saw, link to what's there, and detail why you feel it's harmful. Avoid all appearance of accusation: it's a good way to put folks who otherwise might help you on the defensive, and - if you're wrong - and even better way to kill your credibility.
Don't use comments for anything important
Comments are, by design, disposable. There's no history, no cost or reward, and they can and will be deleted if there's any hint that they're harmful... or even simply not useful.
On the other hand, questions and answers do have a history, and if deleted can even be restored. If you have something important to say, think twice about putting it in a comment.
Remember the big picture
You're shaping this site. At this stage of the game, every question asked on the main site and every discussion raised here on Meta are important: they're helping to set the tone and the policy for what the site will look like a year down the road.
Make the most of that opportunity...