I've done a bit of searching around for this, and haven't found anything similar, so either I am doing something wrong, repeatedly, or other's don't mind/care.
Using latest version of VLC, on Windows, with no special settings or other weird uses. This problem is not version specific, I've noticed it happening for a while. If memory serves me right, this did not used to happen, once upon a time, but my memory is hazy.
I am using SRT subtitles, and noticed a couple odd behaviours.
When a subtitle entry has 3 lines, they will sometimes get collapsed into 2 lines. Not sure why, or what the criteria might be. It's not a huge deal, but often a separate line means it is a separate piece of dialogue, spoken by a different character. So this is a problem, but the actual problem is that when this collapsing happens on a subtitle that is in italics, there will be no space inserted between the two collapsed lines, whereas when there is no markup, there is a space. This makes the subtitles look like a real mistake.
The second problem is alignment. I have the subtitles positioned at "bottom", which is the default setting. Create a simple SRT file with one entry consisting of 3 identical lines, when displayed (assuming they don't get collapsed), the first 2 will be perfectly aligned vertically, but the last line will be noticeably offset to the right a few pixels.
Mostly, I'd just like to know what I am doing or not doing that is causing the concatenating of that 3rd line sometimes.