I was figuring there'd be more enemy resistance, but if anything the closer we get to the core the fewer enemies there are... Don't you think that's strange?
Literal
I [topic-は] more enemy [of-の] resistance [subject-が] exist [quotative-と] was-estimating-[explanatory-んだ][but-けど], on-the-contrary center [to-に] advance [the more-ほど] enemies [subject-が] decreasing-[came-てきてる].... Strange [quotative-と] think-not [I wonder-かしら]?
踏んでた (from 踏む 'to step on' sense 5 — 'to estimate, reckon, guess') is idiomatic for 'I was figuring/reckoning.' むしろ 'rather, on the contrary, if anything' signals that the reality contradicts expectation. ~ほど 'the more X, the more Y' here establishes a proportional relationship between advancing and enemy reduction. かしら is the feminine counterpart of かな 'I wonder,' marking this as female speech. A tactical observation with growing suspicion.