Yes they do. All the time. The 2nd law of thermodynamics places limits on the entropy change of a system depending on the external energy input, it doesn't eliminate the possibility of entropy increasing. If it did, refrigeration (both natural and artificial) wouldn't work.
No explosion has ever produced a laptop computer. No tornado has ever assembled a Rolls Royce. And no random combination of molecules has ever produced life. What is the minimum number of amino acid molecules required to make up the simplest virus? A few thousand? I really have no idea but for the sake of argument lets call it 1000. The number of total possible combinations is 1000! which equates to 4.023872e+2567.
These comparisons don't make any sense. Viruses weren't assembled by random collisions of molecules any more than a newborn baby is assembled by the random collision of molecules. For one thing, peptides with as few as 32 amino acids have been observed to self-replicate in the right environment. Second, your rudimentary calculation ignores the possibility of any very simple selection mechanisms at the most basic level.
An analogy -- if you flip a row of 100 coins repeatedly, it will take you somewhere around 1029 attempts to land all heads or all tails. You wouldn't get it done in a billion billion years. Implement the strongest selection method possible (only re-flipping tails), and you'll probably have all heads in less than 10 flips. Implement a weaker selection mechanism (like only keeping heads when they appear next to other heads), and you'll get something in between these extremes. The chemical behavior of complex organic compounds implements selection mechanisms, many of which we are only beginning to understand, and unless one has specific knowledge of how those selection mechanisms work, it is impossible to generate even a remotely accurate evaluation of the probability that self-reproducing systems (i.e. the precursors of life) could generate of their own accord.
How did the FEWER than 32 get to be 'replicated' or 'changed' into 32+???