Agree with your assessment that "deception" is too harsh of a criticism regarding scientific errors and flaws. The inherent flaw of scientific reasoning is that the method is inductive in character, but the hypothesis/theory formulation (at least in the modern times) tends towards deductive in character.

Unlike mathematics, which is entirely fictional, the purpose of the tool we term "science" is to approximate and describe reality using observable factors. It may be that the OP is discontented with the modern trend of scientists proclaiming "theories" based mostly on deductive reasoning, upon what may or may not be a flawed premises/assumptions.

Concepts such as "parallel universe," "multiverse," "abiogenesis," and "macro-evolution" are deductive reasoning that can never be tested using scientific method. Furthermore, in the realm of quantum and theoretical physics, where the very act of observation skews results of the experiment, the limits of pure inductive methods can be appreciated.