Not necessarily. A great deal of microevolutions are in the soft bits of creatures. Denser musculature, or thicker/thinner hair, or adaptations to the squishy bits that decompose. Not to mention that fossilization requires a very specific set of conditions to occur, so possibly those transversal bones occurred where/when the conditions were less than valid for fossilization.
Also, Darwin's theory isn't the entirety of Evolution as a theory.
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Micro evolution doesn't prove evolution. God created his creatures with a way to adapt. If animals couldn't adapt when, say a natural disaster hit or humans invaded their habitat they would become extinct. Also no evidence of macro evolution has been found. Only micro. And micro evolution doesn't prove evolution
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Macro evolution exists in the form of speciation. The instant small changes hit a point that the original species and the altered version are no longer capable of reproducing, they've become two different species, which is a macroevolution.