Welcome to the forum.
It's hard to say why, because this isn't something that is universal to all cameras. It may be something specific to your camera or this type of camera etc.
Firstly, you need to understand about Depth of Field (DOF). That is the range of distance (away from the camera) that will be in focus for any photo you take. You can control the size (depth) of the DOF by choosing the lens aperture (F number), the focal length of the lens and the distance to your subject.
At some settings, you DOF may be very thin. Your camera probably isn't capable of really thin DOF at normal distances...but as you get really close to your subject, the DOF will get really thin. It might only be a few mm deep. So only a thin part of your subject may actually be in focus, and if your DOF isn't placed just right, your photo will look (be) out of focus.
So to be sure, when you see this problem, make sure that your DOF is deep enough to actually get your subject into it.
And of course, it's reasonable to think that maybe the digital readout of the focus distance, may not be completely accurate...or maybe you're not measuring accurately. So there could be one or more things 'out of whack' that can contribute to your issue.
But the question remains, why use manual focus on your camera. I'd guess that auto focus is adequate for your needs, 97% of the time.