These are common reasons why the automatic internal links defined with the Interlinks -> AIL menu are not applied in the posts, pages and custom post types.
The automatic internal links are disabled
In the Interlinks -> Options -> Advanced menu there is an option named Enable AIL which is used to determine the default status of the Enable AIL field of the Interlinks Options meta box.
If this option is set to “No” the automatic internal links will not be applied to the posts where the Enable AIL field of the Interlinks Options is not manually set to “Yes”.
The correct post types are not selected
The Post Types field available in the Interlinks -> AIL menu allows you to enable the application of the automatic internal link on specific post types.
Make sure that all the post types where you want to apply the automatic internal links are included in this field.
The total number of automatic internal links has been limited
If you are limiting the total number of applications of the automatic internal links that should be applied to a post, only the automatic internal links with high priority (in case of automatic internal inks with the same priority only the first automatic internal links added in the Interlinks -> AIL menu) will be applied.
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A page builder is used
A common problem with many WordPress page builder is that the some of the elements of the page builder are not actually saved in the post, but on external database tables.
The Interlinks Manager plugin doesn’t apply automatic internal links and doesn’t perform analysis on the elements of the page builder saved in external database tables.
More information on the use of this plugin with page builders is available on this FAQ.
The test mode is enabled
With the test mode enabled the automatic internal links will be applied to your posts, pages or custom post types only if the user that is requesting the posts, pages or custom post types has the capability defined with the AIL Menu option available in the Interlinks -> Options -> Capabilities menu.
You can enable or disable the test mode with the Test Mode option available in the Interlinks -> Options -> Advanced menu.
A protected tag or a protected Gutenberg block is preventing the application of the automatic internal links
Sections of the post might be excluded from the applications of the automatic internal links with the Protected Tags and Protected Gutenberg Blocks available in the Interlinks -> Options -> Advanced.
To know more on this subject please check out this FAQ.