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You can fix this by ungrouping the blocks and make the ones that dont match bigger so that they overlap eachother

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Do NOT do this.
This is a bad way of level design in my oppinion.
Instead do NOT use CSG Subtract but build the doorways etc. by hand, its easy and won't end in such gaps.

So listen to what TheFanatik already said.
Thats the way to go.

keep it up its really coming along!