iPad Mini 2 will only charge if turned off first

Have you calibrated the new battery? Sometimes, uncalibrated batteries can cause issues with smart devices. Drain battery below 10%, then charge uninterrupted to 100%.

You may also want to check the specs on the replacement battery if you didn't get it from iFixit, as well as ensure that the proper safety certifications are in place to prevent the iPad from becoming a $500 charred smelling paperweight. Check mAH (milliamp hours) and voltage. If you're having trouble with a non-iFixit battery, try the iPad mini Battery from iFixit (and no, I'm not getting paid by iFixit to say that).

I've also encountered scenarios where the device needed a particular sequence after installing or reinstalling a battery:

1. Turn off the device and unplug the battery
2. Perform a hard reset without the battery
3. Plug the battery back in, and perform another hard reset with the battery.