Missing transactions could be for a number of reasons -:
- The user who has made the transaction had his or her JavaScript or cookies turned off
- The user has left the page before the transaction has had chance to send to Google Analytics
- There might be a JavaScript issue on the order confirmation page
- Your payment gateway provider has their own order confirmation page so customer never come back to Magento order confirmation page.
- Order confirmation page doesn't get loaded with certain payment methods.
There could be a problem with the extension you are using, you might want to give it a go at the following module which comes with the log which allows you to track all your transactions
For Magento 2
https://www.scommerce-mage.com/magento2-google-enhanced-ecommerce-tracking.html
For Magento 1
https://www.scommerce-mage.com/magento-google-enhanced-ecommerce-tracking.html
If you are using Magento 2 the following extension ensures 100% order sychronisation between Magento and GA
https://www.scommerce-mage.com/magento2-google-analytics-missing-transactions.html