We are aware of this issue and are working towards a solution in a future release of Content Matrix.
As a temporary solution, you may follow these steps:
1) In the target, make sure all the Content Types are published at the tenant level:
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2) In the target site confirm you can see the Content Types from the hub:
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3) In the target site create a temporary library to add all the necessary content types from the hub, this will create a local copy making the Content Type available for Content Matrix:
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The site content types are now updated and linked to the hub:
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4) Open Content Matrix Console and migrate the site doing a Copy Site > Paste All Site Content, use "Incremental" Mode and unselect the option "Copy Content Types"