。
But there were mountains of unexplored problems there.
Literal
However there [in-には] mountain-[extent-of-ほど] [genitive-の] untouched problems [subject-が] existed.
Research-narrative sentence. 山ほど ('as much as a mountain,' 'a ton of,' 'piles of') is a set intensifying phrase for quantity, with 山 ('mountain') as the unit of exaggeration. Common with countable concerns, work, or problems. 未踏 (みとう) is a formal compound 未 (not yet) + 踏 (step on) = 'untrod, untouched, unexplored' — originally for geographical frontiers, now used figuratively for scientific or intellectual territory. ~には emphasizes the location. 問題があった = 'there were problems.' The しかし at the start (here in the slightly formal しかし rather than でも) marks this as a conjunctive 'however.'