I'm assuming what you're referring to is the When a new channel message is added trigger. I found two posts on the Power Community forums which may find helpful in diagnosing the issue
- Solved: When a new Channel Message is Added Trigger is not... - Power Platform Community (microsoft.com) where recreating the connector/flow resolved their issue
- Solved: When a new channel message is added triggers when ... - Power Platform Community (microsoft.com) where they inspected the body of the trigger
I'm not a subject matter expert but in your position, with a trigger not going as expected, I would investigate to see if there's any failure in the trigger/connector itself. Or look for any patterns for when it is firing vs not firing when I expect it to. If you haven't already, review Collect diagnostic data for workflows - Azure Logic Apps | Microsoft Learn to gather telemetry and see if anything is standing out.
If you're not referring to the Teams connector, my apologies; I would, though, would look at using three separate logic apps as workaround if I weren't able to determine why the trigger isn't working as expected.
The first would be base app that does the actual processing. This app would be trigger by an HTTP webhook trigger which all I would need to do is send the payload that needs to be processed. For the gaps, I would use a reoccurring trigger to capture any missed messages through either the Get Messages connector or directly from the Graph API, an example is shown in this StackOverflow post which will call the base app through the HTTP webhook.
Also, the Power Platform Community (microsoft.com) is an established community that has more SMEs that are engaged and may better workaround options.