Just having the CSV file to look at, it's difficult to know how to help.
From the numbers it looks like it's something with exactly 90 and 45 degree angles, and it doesn't have an apparent coordinate system so it must be a local coordinate system with ruler measurements.
Also, just looking at the CSV file there's no way to tell how it was imported.
Perhaps you could include a screenshot of the REFERENCE tab values after import, and a reduced image or two, hopefully adjacent, so we can get an idea of the image overlap and number of identifiable points.
I get excellent results with UAV images by using a csv file to specify lat, lon, altitude, heading, camera angle, and platform roll using a CSV file like the attached and continuing with all the steps and settings in the Photoscan tutorial PDF.
Having said that, insufficient image overlap, image quality, identifiable points, and not making sure all the CSV values end up in the proper fields could sure mess up a perfectly good set of images.
Yes, after you load the images and import the CSV values, the next step would be to align photos. If that doesn't work we'll need more info to help understand why.
Hank
Texas