It’s not that crocodiles have their ears in their infratemporal fenestrae exactly, though I can understand why it would seem that way.
What happened is that along the lineage to extant crocs, the eardrum became enlarged and, for lack of a better option for structural support, it became enclosed withing the bony bar at the back of the skull which consequently widened covering in part the infratemporal fenestra.
Here’s some labelled images for further instruction:
Side view of an Allosaurus skull. From Savali, Udo M. (2017, 22 December). BIO 370 — Vertebrate Zoology — Dinosaur Skeletons.
Views of an alligator skull. From Savalli, Udo M. (2009, 22 December). BIO 370 — Vertebrate Zoology — Alligator Skeleton.
You should consider that in general, relationships between bones and soft tissue structures are maintained over the course of evolution. The eardrum in diapsids is closely associated with the quadrate. The quadrate along with the quadratojugal and the squamosal form the bony bar behind the infratemporal fenestra. You can see that the quadrate has a position closer to the midline of the animal than the quadratojugal for the crocodilian: on the dinosaur the quadrate is hidden by the quadratojugal from side view for the most part.
You’ll also note, as alluded before, that the aforementioned bony bar at the back of the skull on the alligator has a much greater width front to back than on the Allosaurus. It expanded forward, forming a wall over part of the infratemporal fenestra, but also backward to enclose the eardrum completely.
Here’s an interpretation I drew up:
Modified from figure 2.B of Montefeltro, F. C., Andrade, D. V., & Larsson, H. C. (2016). “The evolution of the meatal chamber in crocodyliforms”. Journal of Anatomy, 228(5), 838-863, showing the back of the skull of a dwarf crocodile.
As to the why, it seems hearing was fairly important to crocodile ancestors in their daily lives to justify the investment up and to including evolving ear lids to protect the now large eardrums as reported on the above-cited Montefeltro et al. (2016) paper. You can also find there an ample discussion of the background for the above summary.
I do hope this clears up matters. If you have any more questions feel free to ask.
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