When loading command blocks using structure blocks the commands fail to run when loaded into a world. Fixes such as updating the block or reloading the structure block do not work, the easiest way I found to solve it is to put the problematic command block into "Needs Redstone" mode, power it and then unpower it again, and turn it back to "Always active" (If it was originally on that setting)

I found that it mostly effected repeating command blocks, especially if they have a condition: "execute if ..."

The only time I was able to reproduce the bug was for a "Needs Redstone" command block, there is a video of that reproduction in this redit post:
https://www.reddit.com/r/MinecraftCommands/comments/ogx5a5/does_anyone_else_have_problems_loading_command/
I'll update this if I can reproduce any other examples