Starting before yesterday night our catalog.version.updated started triggering hundreds of times every few hours. Is this some kind of error on your side or why is this happeing? usually, we wait to get it once each time we modify 1 item at a time, but this is like someone is mass updating all our items every few hours each day. And the problem is that our 3rd party system is getting all API credits exhausted every time it happens. Attached is an image of the log showing hundreds of times this webhook triggering and the app id is:
sq0idp-H5WaO0g6b5uHOtQI5_kOoQ
When you run a sync on the catalog are you seeing a difference like an item was updated? 
What do you mean by running a sync on the catalog?
We noticed this issue started when our Square website went live. Can there be any feature there triggering some kind of mass update in the catalog? that trigger catalog updates and sending the webhook these many times?
By sync I mean are you calling SearchCatalogObjects when you get an event to pull in any changes to the catalog? Are there any changes to the catalog? You’ll want to identify what catalog objects are causing the events to figure out why they’re being triggered. An event will be triggered when any catalog object is created, updated, or deleted.
