My recent experience is sort of similar. I think the basic problem is that iCloud sync takes a very long time, and until the sync completes the views and feedback are misleading.
My library is fairly large (38,894 photos, 494 videos, 289.98 GB according to the info at the bottom of the Photos window in Photos, 547.13 GB file size reported by Finder). I believe the large discrepancy in reported file size between Finder and Photos is a recent occurrence, but I do not know when it appeared so I cannot say for sure.
Saturday, September 10, my startup disk failed. What happened was not so bad. Friday evening everything was fine. No problems with Photos, my System Library was synced with iCloud, and for my local photos library Download Originals to this Mac was set. I shut down Friday evening. On startup Saturday, the disk with my system and Applications could not be recognized. My Photos library on a different internal disk in my Mac Pro was not affected. I started up from a different disk with a full El Capitan install. I launched Photos, and set it to use the Photos library on the external disk. All well and good, no problem so far.
However, being run from a different system disk, when I set the library as System Library, Photos began a new sync with iCloud. Past experience tells me a sync will take 5 or 6 days. Generally I avoid running Repair Library because a sync is required afterwards, and that takes so long. Since my library was already synced with iCloud the day before, and a re-sync was to be done anyway, I ran Repair Library. The Repair finished and sync began Saturday September 10 at 319 PM Pacific Time.
After the Repair I noticed many photos, in moments approximately from April, June and July 2016, were only represented as placeholders. No image. These were all fine before the Repair. Distressed, I opened Safari to check my iCloud Library. The photos missing in Photos On My Mac were all present in Photos in Safari/iCloud. I scrolled back through the iCloud library to older photos. All were there. I scrolled forward to newer photos. Now many were missing, which had been present just a minute earlier. I waited. The missing photos did not appear.
Today, two days later, the sync is still less than half done. In Photos On My Mac. photo place holders in moments last spring are sill missing images. Photos On My Mac says it has 38,804 Photos, 494 Videos, and is Uploading 24,155 items (140.72 GB of 289.98 GB). Finder tells me my library takes 495.6 GB of disk space. Safari/iCloud/Photos tells me I have 42651 photos and videos, and that the library is updating.
The point is that I started with a library in good shape and synced with iCloud, and ran Repair Library. Now in Photos On My Mac many photos do not show their images, and various reports of items counts and library file size do not agree. To me, this situation sounds somewhat similar to the issue you report.
In the past I had seen similar bizarre incongruities when Photos On My Mac and Photos in iCloud are not synced. In those instances, I waited a week or so for the sync to complete. When the sync was complete, the photos reappeared and the reports of photos parameters such as item counts and file size agreed.
My guess is that the oddities you see will clear up when the sync is done. In Photos on your Mac, what do you see in Preferences/iCloud? How is your sync coming along?