There are a couple reasons you might see tweets in a report that don't show up in a Tracker. 

1) Snapshot reports - both the free and the full versions - analyze recent historical tweets. Trackers find and analyze tweets in real time. So, depending on when you ran the report and set up the Tracker, you might be looking at two different sets of tweets. Trackers will not include tweets posted before you set up Tracker, and reports will only include tweets from the past 4-5 days. 

2) Reports use the Twitter Search API and Trackers use the Streaming API. In some rare cases, these APIs handle tweets differently. For example, right now the Search API auto-expands some shortened URLs to analyze the destination URL. If your search query appears in the destination URL, that tweet might appear in your report. The Streaming API does not do this, so that tweet would not show up in a Tracker. 

3) Tracker search queries need to be very literal. This includes punctuation (more details here about writing Tracker queries). Some report queries handle punctuation less literally, so you might get more results for a report search query with punctuation. Our best advice to get around this is to test your queries first with a free report before committing to a full report. And in Trackers, user quotation marks around your queries with punctuation to be sure we find exactly what you're looking for. 

If you ever have questions about the data in your reports or Trackers, please ask us! Twitter changes small things all the time, and we do our best to stay up-to-date on how things work at any given point, so we're happy to help you figure it out.