Lily when your roof was installed what did the tear off consist of ?Was it a layer or two over woodshake resulting in a redeck? Meaning that it had woodshakes under other layers and it required all new plywood ? The reason i ask is because it looks like to me another case of NOT offsetting the plywood by 4', what that means is generally when plywood is installed a full sheet(4'x8') is installed the full length of the gutterline, then when you start another course of plywood instead of a full sheet you would put in a piece that is half of the size of the first one.(4'x4') You would do that along the whole entire roof. if it was installed by the method of stacking,(no offset)
that is wrong. When the company told you that it was normal was they with you looking at your home? The reason I ask is usually during late fall thru febuary the shingles conform to how they were shipped and loaded..,I am not making excuses by any means.,Sometimes after a new install during winter months it takes twice the time to lay down and conform to your roof and that may have been the reason they had said that to you. But if they were looking at the house and said that then they were snowballing you. Also if they were not the installers of the plywood then they cannot be held 100% accountable for that,.but they should assume most of the blame and the reason I say that is they were to provide a service for you in a professional manner.,When and if they noticed it then you should have been contacted immediately and given the option to correct it before the shingles were installed, its sorta like taking your car to a dealership for service like changing the oil and the guy changing your oil whille putting the car on the racks had noticing that 3 out of 4 of your tires have wire coming thru and taking your money for the oil change and saying nothing about the tires.Yes H-clips should have been used, the clips keep the plywood around 1/8"-1/4" apart for several reasons one being during the seasons the plywood expands and constricts and if the gap isn't there then they buckle and contort.Also its gapped because your house is always shifting,so naturally the gaps are needed.And unless that plywood/O.S.B was in the rain for several days of constant rain it would be o.k because according to the plywood institute
they actually think its better for O.S.B to get wet a couple times due to the fact that if clips are not used and the plywood was installed then when it dries out it can expand.and buckle too.Lack of ventilation can also cause the plywood to sweat underneath and dry out and buckle.Yes, the shingles look like some of lowes material.From may view they do look like some owens corning classics, which are 20yrshingles, and as far as the water running down the siding it very well could have been a blow thru on the edge, a blow thru happens majority of the time in the winter months and the nail blasts thru the shingle because of the cold and not paying attention to air pressure., and if I were you have someone unaffiliated with the contractor and look between the seams of the plywood and make sure felt was used.
Sorry for the novel