The short answer is that this happens when your hashtag has been (automatically, by Twitter) deleted from the re-tweet Here's a little more detail and and explanation of how/why this can happen:
Twitter allows two types of re-tweets. "New Style" and "Old Style". The issue of lost RT's usually occurs with New Style re-tweets when the original tweet length was the full 140 (or close to the full 140) characters allotted, and the hashtag was placed at the end of the message.
Hashtracking: We have a really important message that we want you to retweet and we have this really important hashtag that we're sticking at the #ENDHERE
If a user RT's the above message using a New Style retweet, the tweet looks like this:
RT @Hashtracking We have a really important message that we want you to retweet and we have this really important hashtag that we're sticking at….
Note that the message has been automatically truncated and that the hashtag has been dropped due to space constraints. Once the hashtag is dropped, the message cannot be counted in your hashtag report.
Old Style retweets offer users the ability to edit a retweet message, however the same issue can and will occur if your message goes over the 140 character limit and the hashtag is at the end of the message - it will be truncated, and the RT message will not show up in your hashtag report.
Some ways to avoid this problem include keeping your messages shorter, and placing your hashtag closer to the beginning of the message.
While our reports, and Twitter's search functionality will not show you the retweet count for truncated messages in a hashtag search, the count for new style retweets of any particular tweet are available on the homepage / unique URL for that original tweet. You can access this page by clicking on the time stamp for that tweet.