I am considering applying for US PhD Program. In the UK, at many unis the first year does not count towards degree classification. Is this known in the US? Will they be wondering why I stated I have X %, but they calculate Y % ? Shall I explain to grad school admissions that 'the first year didn't count' towards my degree classification?
For the benefit of non UK members, the first year marks of a degree at a UK university is not used for calculating a student's final grade. The only requirement to continue on the degree is achieve at least 40%. It is therefore not uncommon for students to achieve marks in their first year which do not reflect their full abilities, and while it does not affect their grades it can affect how future employer or post graduate admissions view their application!
If this is the case you should address this in your personal statement. Tell them how you gained a new perspective and work ethic after your first year at university and demonstrate this with your improved results in your subsequent years along with appropriate participation in university clubs and societies.
If however your first year marks are consistent with your subsequent years, there is no need to mention it. Your application is about you as a potential student, not about explaining the intricacies of UK grade calculations.
Edit: The reasoning behind only requiring a mark of 40% for the first year is to allow students some adjustment to a more independent study style and also to give young adults entering university the freedom to have new life experiences outside of academia. The prevalent philosophy at UK institutions is that academic achievement is not the only goal of attending university (though it is obviously still important!)
Since the progression of students enrolled on a degree is decided on a department by department basis its impossible to find a single decree stating this how all UK universities operate it is by far how the majority work. Provided below are links to progression guidance from 2 UK universities, stating that only pass marks (40%) are required and that this mark will not be used to calculate degree classifications. University of York Progression, University of Durham Progression