When a subcategory is enabled and set to "Include in Menu" AND the parent category is disabled or set not to "Include in Menu" the subcategory is included as a top level menu item.
Please note, it appears this issue was added via the following commit:
https://github.com/magento/magento2/commit/026a599577b45097f237d3acaf24bae347bd8e11#diff-b1fa678d0cae299f35fb1633bb9dcf5c

Thanks for reporting - internal issue is MAGETWO-72112
@toddwolaver thank you for the report. The issue already fixed in 2.2.0
@okorshenko - I just upgraded to version 2.2.5, which seems to be latest version of 2.2 available. However, the bug as described is still there. In what exact version of 2.2 is this supposed to be fixed already?
Having same issue on Magento 2.2.2 Enterprise Edition.
Still exists in Magento 2.3.2 CE.
@okorshenko This issue is still there in Magento 2.3.x. Anyone have solution for this ?
Encountered this issue on 2.3.3 just now.
Hi @engcom-Hotel. Thank you for working on this issue.
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Hello @BezV8
I am not able to reproduce this issue on the Magento 2.3.3 & 2.4-develop.
Testing scenario:

Result:
There is no disabled category in top menu as expected:

So i have close this issue as not reproducible.
Could you verify my steps?
@magento give me 2.3-develop instance
@engcom-Hotel I have just tried the same methodology as you on a 2.3.3 site we are developing and the subcategory does show on the menu even when the parent is set to not show.
I have yet to test on a completely vanilla instance.


@BezV8 i tried again with enabled top category and a child category is not visible:


@BezV8 i think it is related to your custom theme(some category display layouts is broken). Please try to find different of your theme layouts and Luma theme. Hope it helps.
So now i have to finally close this issue as not reproducible.
Thanks for collaboration!
Hi @BezV8. Thank you for your request. I'm working on Magento 2.3.3-develop instance for you
@engcom-Hotel I managed to track the issue down to a custom extension, removing that fixed it.
Most helpful comment
@okorshenko - I just upgraded to version 2.2.5, which seems to be latest version of 2.2 available. However, the bug as described is still there. In what exact version of 2.2 is this supposed to be fixed already?