There are many questions that need to be answered in science. Critical thinkers are people that recognize these questions, which are sometimes problems or imperfections in an existing scientific theory. Although there are not always answers to every problem, the first step is acknowledging that there is a problem. These are some of the flaws that can be found in mainstream theories.

Plate Tectonics
The earth is not only expanding, but it is ganing in mass meaning gravity has increased slowly over the millions of years

Black Holes
Black holes as described by Big Science are very problematic

Special and General Relativity
Even the scientific "genius" of our age is not immune to being wrong

Big Bang Theory
The Big Bang is under attack and is being abandoned for a steady-state universe

Real Number System
There are no negative numbers in physics

Quantum Mechanics
Quantum Mechanics has gone off the deep end

Stars are gaseous
What are stars really made of?

Dark Matter
Dark matter is not needed according to critical thinkers outside the mainstream

Particle Physics
Many critical thinkers believe that most of particle physics should be thrown out, others propose new models to greatly simplify it.