The neuter genitive singular comparative of clarus is clarioris. Why is this? Shouldn't it be 'clariusis', since the form of neuter adjectives in the comparative form ends on -us?
This phenomenon is not unique to comparatives. For example, the genitives of tempus and lepus are temporis and leporis, while you might expect tempusis and lepusis. You can simply learn and accept that the stems of these nouns are tempor- and lepor- without further questions asked. This is what I would suggest as a starting point for anyone.
While mostly unnecessary for the ability to speak and use Latin, it is interesting to wonder why the stems are as they are. (I assume this was your core question, but I may have misunderstood.) The nominative and the stem used to be alike as you might expect; they were *tempos and *lepos. In the nominative the o changed into u in the same way as in the second declension nominative ending -os > -us. When an ending was added, the singe s ended up between two vowels. In this case rhotacism kicked in and converted the s into an r. This lead to the genitive forms temporis < *temposis and leporis < *leposis. Now the o was no longer subject to the change into a u.
That is, the nominative changed from tempos to tempus and the stem from tempos- to tempor- and similarly for lepus. This might lead to more questions than answers, though. Why did the sound changes work that way? Whatever the reason for these changes was, these patterns of sound changes are common in Latin and the weirdness you observed in the comparative fits nicely into a bigger picture of the evolution of Latin.
Th neuter adjective clarius is of the third declension, just like words such as praeceps (gen. praecipitis) and vetus (gen. veteris). As you can see, the genitive is often quite different from the nominative in words of the third declension. You can't really predict the genitive form based on the nominative form unless you know quite a bit more than just the common endings. You need to know the stem of the word, which is often not (fully) visible in the nominative singular.
Secondly, the rule is that masculine and neuter words differ only in the nominative and/or accusative: in the other three cases (genitive, dative, ablative), all endings must be the same between masculine and neuter. It follows therefore that the genitive singular of clarius must be the same as that of clarior: clarioris. As a rule, this applies to other Indo-European languages as well.