The data in the Battery Saver needs to be interpreted carefully. Notice that 56% and 44% add up to 100% - certainly your Messaging app wasn't the only one that is running for it to consume 100% of the battery power. Rather, those two values must be interpreted in conjunction with the summary of app usages under the main Battery Use page.
For example, in my phone, the summary of app usages (the long list with different apps) tells me that my Messaging + Skype has used 11.1%. Tapping on "details" brings me to a page where it says "In use: 41.9%" and "Background:58.1%". This means that this particular app used 41.9% of the 11.1% while it was active, and the remaining 58.1% of the 11.1% in the background. Notice how these two values also add up to 100%.