Even with a relatively low usage, it's possible for apps without explicit request limiting to occasionally hit the secondly limit if a certain action/subset of actions triggers a number of different processes. For example, if your app were to make a request every time a contact is updated in HubSpot, you might not normally hit the secondly limit. However if a user bulk edits a few dozen contacts, you could easily hit the secondly limit (since the updates will all happen concurrently).
The simplest solution would be to sleep for a few seconds before retrying a request that hits the secondly limit. You could also batch certain requests like contact/company/deal updates, which can help avoid the secondly limit. The following developer doc also has some tips for working within the rate limits:
edit: If you'd like me to investigate your traffic, can you give me your appId and the Hub ID of the portal you hit the limit for?