Hero of Night and I are currently playing the Beta, and we found a chest in a small cave in Skywatch that could not be opened.
When prompted to hold Square the blue circle fills, but at around 80% it stops and 'backs out'.
We tried leaving the area and coming back, punching, and a Fist of Havok, but to no avail. There was no loot found this day.
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I can't remember where but in the second story mission I found a big one in a tiny cave, and it did as you described. It also dissappeared shortly after I tried.
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Me and a friend had exactly the same issue in the area with the giant map you have to scan. Got to about 80% full then nothing. After about 3-4 minutes of trying it disappeared.