Paleontologists have created phylogenies (nested hierarchies) that trace extant species back to common ancestors.
Biologists have created phylogenies using mathematical techniques that operate on two classes of data: characters and genomes.
All three types of phylogenies are almost entirely in agreement with one another. (Indeed, scientists would expect stochastic processes to occasionally produce anomalies, just as flipping a fair coin might produce 15 heads in a row, which would strike most folks as evidence of an unfair coin.) Long story short, the fossil record and the genomic data agree on the evolutionary pathways.
Thus I have no idea what you are thinking of when you say that paleontologists think the fossil record refutes evolution. Perhaps you could cite actual quotations from paleontologists who have published research in peer-reviewed journals so we can compare notes.