There are a number of main problems or questions for evolution theory. New evidence or interpretations of studies will continually bring further issues and perhaps modification of the theory of evolution or the dismissal of the studies results.
Molecular Clocks are normally used to date fossils when there is little or no geological material to do it. Fossils can be dated by the number of mutations in their genes. Molecular clock dating results have previously shown that fossils are much older than the geology time for them.
Post Gondwana evolution and the Green Web
One of the more accepted parts of evolution theory is that similar forms of life are found in different countries because these use to be connected in a supercontinent. They original evolved on that supercontinent then have again evolved in their now separated country.
These land masses were once joined in Gondwana, and one famous school of thought, known as vicariance biogeography, holds that the modern distributions mostly result from the subsequent separations of the continents and the organisms that lived on them.
On the other hand, molecular 'timetrees' increasingly place many evolutionary events after the final breakup of Gondwana, about 45 million years ago.
Turn back the molecular clock, say Argentina's plant fossils (psu.edu)
Problems with evolution theory would include if molecular clocks are found to be correct, or even one set of results (older or younger fossils).
There seems to be evidence or studies that interpret life forms evolved after Gondwanan rifting occurred. Plants like sundews can also create problems, both for and against the argument.
Evolution theory problems - the problem is dating methods?
Could the issue with fossil dating by molecular clocks perhaps show that genetic mutations can be slowed down or increased?
If these results could be effected then could Earth clocks by Isotope analysis of things like carbon dating also be skewed?
Another problem for the theory of evolution is the whole Big Bang and planet formation theory. Could it be an Electric Universe or could we have had an Expanding Earth?