This might be done on purpose anyways, but I happened to find this by chance and thought it was very interesting.
For whatever reason, cobblestone walls will not connect to fences, but they will connect to fence gates. I happened to place one down beside it and interestingly enough, the fence gate aligned more to the wall, which is at a lower level to the fence, which still connected, making this strange looking level. Thought I might mention it in case it is a glitch, but it's fascinating how the fence gate decides to align to the height of the wall instead of the fence, and both wall and fence still connect anyways.
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Btw,
Your game, launcher or server is modified.
If you have any issues, they should be reproduced in a vanilla environment before being reported here.
+ Any non-standard client/server/launcher build needs to be taken up with the appropriate team, not Mojang.
+ Any plugin issues need to be addressed to the creator of the plugin or resource pack.
+ If you have problems on large servers, such as The Hive and Hypixel, please contact them first as they run modified server software.
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This is a bug tracker, not a tracker for "interesting behaviours". Everything you described is intended and it was done on purpose. Also, see MC-2938.