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can you share the steps to reproduce this?

1. Create an api call in postman to a make.com webhook. 
2. Attach that webhook to HTTP module which makes a post request to /call endpoint to make an api call. 
3. I have variable set in system prompt for the assistant which takes in this data. 

The api request has to make.com hook has 
{ 
    "questions" : [ {}, {}, {} ]
} 

Which is passed on to http and then it changes to 
{
    "assistantOverrides" :
      {
           "variableValues": {
                                "name": "{{1.name}}",
                             " questions" : [{{1.questions}}]
         }
     }
}

Your passing them as object instead of stringified.

can you share your assistantID for confirmation.