One can only assume that the creator of the sub has pre-produced everything and did not notice or cannot resolve the issue in general, which is why the layout is always incorrect, or that this layout was intentional...
Hello Cankerworm2012,
You will most likely have to read from bottom to top, no matter how annoying it may be. It is very unlikely that the subtitles in each episode have the wrong layout. Below, I have translated a relevant section of the German FAQ for you:
SUB/DUB (Subtitles/Dubs)
“Can you create subtitles or dubbing for anime XY?”
No, we do NOT create subtitles OR dubbing, so we only have what already exists. Either subtitles/dubbing from official sources or FanSub (handmade FanSubs).
If you want more detailed information, Cankerworm2012, then it's best to translate and read through the FAQ, which you can find under Community Questions (where you asked your question) under the user Star-Geist.