I have a project with one tracker.
For this tracker are only 2 custom fields enabled.
The most custom fields are for all projects.

If I look in field permissions for all roles and this tracker I only see 2 custom fields.
If create a new issue and edit this issue I see only 2 custom fields.

In bulk edit I see 4 custom fields. I don't see a reason why exactly these 2 are there.

Field: class="bool_cf" id="issue_custom_field_values_6"¶

Field: class="string_cf" id="issue_custom_field_values_16"¶

Field: class="string_cf" id="issue_custom_field_values_31"¶

Field: class="string_cf" id="issue_custom_field_values_32"¶

1+2 are additional
3+4 are in this tracker