There is no rule against commenting more than 3 times in a thread. Sorry if anyone has gotten this impression.
However, among the 10 "Recent Comments" visible in the sidebar at right, usually no more than 2, rarely 3, and never 4, should be yours. This is meant to ensure no one person dominates a thread; it gives others a chance to respond to others' responses. One-line comments that quickly correct an error may be common-sensically excepted from this rule.
You need not refrain from commenting, just wait a bit.
I've voiced my annoyance with the commenting system in the past, in particular that it is non-threaded and so often very difficult to figure out what someone is responding to if they don't include context (which they often don't), so I won't give details again.
On the topic of the 2 of 10 rule, if it's to prevent one person dominating a thread, shouldn't the rule be "no more than 2 of last 10 should be by the same person in the same thread" (so 3 posts by the same person would be fine as long as they are in 3 different threads)?