I think you are right there. The bees try to fill all the gaps, but sometimes there are little gaps. The bees will in time fill these gaps with wax.
As Rod has said, check your access point so the bees can recycle the honey. If the honey building up in the trough, pull out the cap and make sure the little leak back point is free from wax so the honey will drain back to the bees to reuse.
You can also loosen the cap a little to make the gap bigger or spin it around a bit to break any wax to help the honey leak back into the hive. The upside is you can taste the honey.
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