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Created a Flow by using the below REST call and stored the title and Urls in another list

/_api/web/lists/getbytitle('DO_NOT_DELETE_SPLIST_TENANTADMIN_ALL_
SITES_AGGREGATED_SITECOLLECTIONS')/items?$select=Title,SiteUrl

Here the problem is it is returning only 100 items but I have 360 site sollections.

Not sure what I am doing wrong

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That is indeed default behaviour. SP by default will return 100 items.

If you want more than 100 items, you need to specify that using $top param.

So you can append, for example, $top=1000 to the endpoint.

Modify the endpoint as below:

/_api/web/lists/getbytitle('DO_NOT_DELETE_SPLIST_TENANTADMIN_ALL_
SITES_AGGREGATED_SITECOLLECTIONS')/items?$select=Title,SiteUrl&$top=1000

This will fetch you the first 1000 items. You can do this upto 5000 items.

If there are >5000 items, you will need to implement paging.

Reference - Page through returned items

How to get more than 5000 items from SharePoint Online in Flow

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