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This is a limitation of the Search API. Twitter says:

Before getting involved, it’s important to know that the Search API is focused on relevance and not completeness. This means that some Tweets and users may be missing from search results

There has been some research looking at the impact of this:

We find that the search API over-represents the more central users and does not offer an accurate picture of peripheral activity; we also find that the bias is greater for the network of mentions – González-Bailón, Sandra, et al. “Assessing the bias in communication networks sampled from twitter.” Available at SSRN 2185134 (2012).

I was able to replicate the issue you were having and I’m confident this is Twitter API limitation rather than the script used in this template. I would usally say it would be safer to avoid the operator and collect in separate sheets and merge the data at a later date, however, I discovered even this isn’t fullproof e.g. on the readme/settings sheets for these archives I’ve included a count of the hashtag occurrence in cells C19:C22 linked to a summarized below:

As you know the data better anything you can spot in the last one?