beachgirlok - Windows Leaking - Now Pulling Off Rock
There is no way to know what is actually causing the leaks just from the photos and your description but here are some observations that might point you in the right direction.
The type of house wrap is unfortunate because it is a woven and coated polypropylene fabric with micro-perforations. It will be considerably less waterproof than non-woven (spun-bonded) non-perforated polyethylene and polypropylene like Tyvek, Typar and others. (Drape a piece of it over a bucket and put several inches of water on top of it overnight) Micro-perforated woven house wraps are also more susceptible to abrasion. The most serviceable wrap behind such rough stonework is Tyvek CommercialWrap.
All vertical and horizontal house wrap laps are not taped as instructed by the manufacturer.
All abrasions and tears must be repaired. Usually a horizontal slit is made and a new piece of house wrap is inserted in shingle fashion and taped. This can also be done with self-adhering flashing. If the damage is extensive a larger area should be removed and replaced.
Corrugated masonry veneer ties have an unfortunate tendency to allow water to be transferred from the back face of the masonry to the back-up wall especially when they are installed pointing upward as shown in the photos. Such ties must be installed with the masonry end higher than the end at the back-up wall therefore it is best to install them pointing downward or better yet, to upgrade to adjustable wire ties like the commercial construction industry did 25 years ago.
If the window is the type where the nailing fin is mechanically attached to the window frame (instead of both being made of one material), then it must be sealed either with a bead of sealant or covered by the edge of the flexible self-adhering window flashing.
The wrap at the window head appears to have been installed behind the nailing flange and the flexible self-adhering flashing appears to have been applied over the nailing flange. This detail might work at the jamb but not at the head. Water that might get behind the wrap from above would have an unobstructed path into the building.
The masonry sill and head details are not shown so I cant comment on them but it appears that there is no sealant at the window jamb-to-stone joint. Mortar in contact with the window frame will crack and actually draw water into the cavity at this very sensitive location. A backer rod should be used behind the sealant at this location if it is expected to last more than a few years. Some residential windows designed for siding application do not provide a frame extension deep enough to support a backer rod at this location. This can be a serious problem. Also, the masonry detailing below the window sills will be super critical for keeping excessive water out of the cavity.
I am curious who designed and detailed the house because the problems seem to be based on more than just poor workmanship.
Hire an architect and someone with impeccable waterproofing credentials as consultants and carefully document everything from the beginning of the project. I suspect you will need all of that testimony and evidence in court later.