We have created a custom 1:N relationship between Account N Contact. When user is clicking on the icon "Show Associated Record" for the Contact Subgrid, records are visible correctly in the Associated view screen. This is reproducible in vanilla environment.

Observation
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Contact Associated View always displayed records which are created by the OOB Contact grid.

Workaround
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Instead of clicking "Show Associated Records" button on the inline grid, add the relationship to the form as a side navigation and then access the related records from the navigation item on the navigation bar for the current account.

Repro Steps
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1. Create a new CRM Online organization (with sample data).
2. Navigate to Sales >> Accounts. This will open the Account homepage.
3. From the command bar (...), select customize entity. This will open the default solution in pop-up.
4. Within the default solution pop-up, Navigate to Account >> 1:N Relationship. This will open all existing 1:N relationship.
5. Click on new 1:N Relation to create a new custom relationship between Account & Contact. This will open the relationship editor.
6. In the relationship editor, select/enter the below properties and click save & close.
-----------------------------------------
Related entity: Contact
Display Name: Custom Account
Display Option: Use Custom Label
Custom Label: Custom Related Contacts
** Let all the other fields as is.
-----------------------------------------
7. Click Save & Close to close the editor and hit publish all customization.
8. Within the default solution pop-up, Navigate to Accounts >> Forms. This will load all the forms in the right pane.
9. Click on Account form. This will open the Form editor for Account form.
10. Within the Form editor, click the ribbon tab insert and then Subgrid to create a new Subgrid. This will open the Subgrid property window.
11. Within the Subgrid property window, Provide the below mentioned required details and hit Set-
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Name: CustomContacts
Label: Custom Contacts
Display Label..: Yes
Record: Only Related Records
Entity: "CustomRelatedContacts (Custom Account)" (This is the 1:N relationship which we created above)
** Let all the other fields as is.
-------------------------------------------
12. Hit Set. This will close the Subgrid property window.
13. Within the Form editor, hit save & Publish.
14. Close the form Editor.
15. Within the default solution window, click Publish all customization and close the window.
16. Again navigate to Sales >> Accounts and open any account record and locate your custom Subgrid.
17. Click on '+' sign to add records.
18. Select any existing contact record. You may be prompted to create a new contact instead of adding an existing. If so, create the new contact instead.
19. Click on icon "Show Associated record", this will open the Contact Associated view screen.

Actual Result
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The Contact associated view screen is not displaying correct records which are there in the Custom Contact Subgrid.

Expected Result
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The Contact associated view screen should show all the record present in the Subgrid.