Diffuse these situations without adding to a perceived disparity. A simple comment to the tune of "oh, my daughter is at the right age, not my son" would probably have been the best bet. Treat these situations as simple oversights, don't teach your daughter that she will be prejudice against or that she will need to be catered to.
You have encountered something that will eventually fade into the background. The person at the booth made some kind of mistake, either in determining which of your children was more interested, at the correct age, whomever was more vocal, enrollment demographics, etc. It's also possible that the booth operator was prejudice against your daughter.
Once she is in highschool she will be bombarded with STEM organizations and fields of study fighting to win her. If you son gets the same test scores and applies to the same programs she will still be offered many more scholarships as your son. This is because the STEM fields are lacking, and therefore are demanding more women.
Let's not be ignorant of this, women are pandered to by the STEM fields, this may or may not be taken as demeaning in itself to a young woman looking to see where she should find herself in the future.
For your son, there will be absolutely zero incentive other than his own interest in the field to pursue a STEM course of study. Your daughter will be given scholarship incentives. There will be special allowances that will give her an advantage. She doesn't need this advantage, but society has decided that she does.
This isn't a prejudice or bias on my part, it's speaking from experience.
Do a scholarship search: http://www.google.com/search?q=scholarship+search+women+in+engineering
The same prejudice that possibly directed the booth operator to give your son the experiment kit instead of your daughter will cause the world to cheer for her instead of your son.
My advice to you is to ensure her that she is not the underdog. That she does not need special treatment. If a boy is preferred over her for whatever reason that does not mean that a boy will always be preferred over her, and she can succeed. Next time she visits a similar booth she can dazzle the operator, she can outscore on the tests, she can figure out complex problems. She doesn't need pandering, when your son gets recognition he deserves or does not deserve instead of her that does not devalue her. She does not need special gear.
Life will not always be fair, but she will succeed anyway.
It's all wrong of course, but she will eventually benefit from this prejudice.