The idea is that the initial tRNA was not specific enough and only care about the first two letters of each codon and ignored the third. So for example Proline was determined by the first two letters CC? and was associated the four codons CCU, CCC, CCA and CCG. Actually, this is the current mapping.
Other blocks of four codons were split for some reason. We can imagine that originally Isoleucine was determined by AU? so initially AUU, AUC, AUA and AUG encoded Isoleucine, but now only the first three encode Isoleucine and the last one encodes Methionine instead.
and then make the whatever letters also important with a almost backward compatible code, so in most case it still doesn't mater, but in a few cases it is important.
[Note: The official letter for whatever is "N" instead of "?"]
That's a great explanation! To add a cool point, the wobble position is frequently modified by highly specific enzymes to make it matter more. It's like some random protein mutated to do this modification and all of a sudden the organism got more RAM thus increasing it's fitness.
Other blocks of four codons were split for some reason. We can imagine that originally Isoleucine was determined by AU? so initially AUU, AUC, AUA and AUG encoded Isoleucine, but now only the first three encode Isoleucine and the last one encodes Methionine instead.
This is somewhat based in the blocks of four codons that follow this patter where the first two base determine 16 block that sometimes are split https://en.wikipedia.org/wiki/Genetic_code and because the third base in the tRNA is strange https://en.wikipedia.org/wiki/Wobble_base_pair
Anyway, IIRC this is a reasonable speculation but it's not confirmed. So don't take this explanation too literally.
With this idea, the initial DNA could evolve for a few (zillions) years as list like
important-important-whatever-important-important-whatever-important-important-whatever-important-important-whatever-important-important-whatever-important-important-whatever-important-important-whatever
and then make the whatever letters also important with a almost backward compatible code, so in most case it still doesn't mater, but in a few cases it is important.
[Note: The official letter for whatever is "N" instead of "?"]