That's how it's supposed to work. Not really. Go to Messicks.com and look up the brake shaft boot under New Holland Online Parts. Pry it out and tap it back in like your're installing any other seal. Best to do both sides. Hard for me to tell if the fluid in your center housing is a bit milky. If that's what I'm seeing, pull the drain plug, let her drain for a few hours, and replace the fluid. If your center housing has water in it (milky), your transmission is worse. Drain and replace the fluid in both. When you put the boot back, put some electrical tape over the threads on the brake shaft and everywhere else the shaft will snag on the new boot and damage it. No use doing the job again. The problem you're facing is an easy fix. Don't sweat it. There's aftermarket boots available online as well. When you figure out your part number, you can shop around and save a few bucks if you wish.
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