Take a close look and...
In Photos 2-4, what you can see are divots, dimples and wrinkles. Which one is it? Without cutting the floor how can you ascertain the cause of the problem? Look at everything else relating to the job site. Using the metal bar tap test, tap on, around and across the planks in the area of the divots and listen for hollow spots. This will tell you if your underlayment is tight to the subfloor or if your floorcovering is not adhered to the underlayment.
Photo 5 shows the offset of the end seams to be less than 6 inches; is this the reason for the problem? I think not. But if the manufacturer states a minimum of 6 inches, then you had best follow the instructions. Not only should you offset for structural integrity but for aesthetic reasons as well. The look you want is one of random uniformity,so don't have a 4-inch offset repeat itself throughout the job; have fun with it and mix it up.
So what else could be suspect on this job? Proper open time for the adhesive? Certainly this is a consideration, as most solid vinyl adhesives require 30-90 minutes prior to setting the planks. If you get into the adhesive bed too soon, then you will have slipping planks and if you're going over a non-porous subfloor, the adhesive will take forever to cure. But what about rolling properly? You can sneak a peek like in Photo 6 at the air vent. What do you see in this photo? Well, I see very well defined trowel ridges, which tells me that the installer either rolled it late or did not roll it at all! But even with this observation the planks where adhered very well to the wood subfloor.
So have you drawn a conclusion yet? Sometimes it is really hard to come up with the proximate cause but take a close look at the size and shape of the divots. They sure look a lot like...kneecap marks! That's right, when you work on the floor covering you have to use kneel boards to help disperse the load. This will decrease the point loading from you knees and minimize the impressions/depressions in the floor covering, especially if you lay in wet adhesive and don't roll with the proper weight roller. Now don't misunderstand what I'm saying; the manufacturer's installation instructions should always be adhered to but if you have no other alternative do what you have to do to insure the desired results, which are a happy GC and a very happy end user. Thanks again for reading: "You Make the Call." Have a great day!