Sure, mistakes do happen, and if you truly found yourself running late or simply couldn't avoid it, that is a different issue all together. Enter discreetly, politely excuse yourself or apologize if you can without disrupting, then move on like it never happened. Everyone else will forget about it if you show you can too. If you fuss and fret, you are perpetuating the disruption by accentuating it. Own the mistake, then let it go.
Just about everyone is the recipient of passive aggressive at some point or another. Here's a tip on how to handle when it comes straight at you: politely hit it head on. For example, I'll say, "The expression on your face is telling me you are not satisfied. Tell me what's bothering you." Or if someone comes in late to your meeting, you can say, "Good, I'm glad you're here - we missed you at the beginning," but make sure you are genuine and then move past it quickly without placing too much emphasis on the issue. If you find that you are angry and can't pull off a genuinely polite reply, try to refrain from showing your discomfort and just wait until you cool off to decide if you should address the issue at all. In other words, if you can't say anything nice, don't say anything at all...but don't roll your eyes or huff and puff - it's simply not professional and you may lose respect from others in the room.
Last thought: a professionally polite, direct response to passive aggression is a great way to gracefully earn respect. Show you can handle it, won't be walked on, but maintain your composure by keeping your cool!