In this answer, the author argued that plants are green instead of red or any other color because of some limitations of the evolutionary process. what are other examples in which the physical and functional characteristics of an organism were a direct result of limitations of evolution?
The "limitations" of evolution is somewhat subjective, but a couple of the important ones include random mutation, "greediness" (chasing short-term advantage), and environment.
Evolution is a complex process by which mutations occur which either 1) benefit an organism, increasing reproductive success or 2) harm the organism, decreasing reproductive success, or 3) cause no noticeable change. Over time, these collected mutations bring about significant phenotypic changes. There's no goal or underlying purpose, though. In your example of plants, chlorophyll could certainly have evolved a structure that absorbed light in different wavelengths, but they ended up doing just fine with their current absorption spectrum.
Another example is the difference between the vertebrate eye vs the octopus eye. For mammalian eyes, the optic nerve covers part of the retina. This is commonly known as the "blind spot", and has obvious negative consequences. For Cephalopods, on the other hand, the optic nerve is located behind the retina, so they have no blind spot.
Both of these examples are the result of random mutations coinciding with ideal (or non-ideal) environmental situations. The author of the post you cited is accurate to say that evolution is not an engineer, working towards a goal. The only goal of evolution is "What maintains life?" It's merely millennia of trial and error, and occasionally calamities occur, causing extinctions and loss of genetic potential.
I really think ANY characteristic of any species you care to name could be considered a result of evolution's limitations.
The term you are looking for is evolutionary baggage.
An easy example is the crappy color vision in mammals and to a lesser extent primates, for a long time mammals were only small nocturnal insectivorous (or at least that is all that survived), during this time mammals lost two of the light sensing pigments in cone cells, leaving only two, primates had a strong enough pressure that a mutation creating a new pigment was favored giving use three, however two of them are very close to each other and overlap, and a whole portion of the spectrum is still invisible to us (ultraviolet) but non-mammals can see it. Birds see colors everyday you and I will never see.
Another mammal example is we turned the gene that would let us keep growing new teeth into control genes that give our teeth complex shapes, which was an advantage to our ancestors who were tiny short lived insectivores, but now mammals can't just grow new teeth to replace old ones like everything else can. there is no way to get these genes back without re-evolving them from scratch or giving up genetic controls on tooth shape, the first is simply to unlikely to occur and the second would be too detrimental.