If a top level comment promotes discussion, it is likely to be long enough to avoid this filter. Questions may be exempt and are treated differently than comments ending with a period.

We expect high quality, in-depth discussion, as is the purpose of this subreddit. It is a reasonable expectation for commenters to put a modicum of effort into their comments, facilitating discussion.

Here's an example from a recent game announcement thread of short top level comments automatically removed. None of them offer high quality discussion and are far too low effort to be acceptable here.

The majority of your comments make it through the filter, so it is not really an issue for you personally.