The core of your question here is that you input a yearly salary, break that down to an hourly rate, and then use that hourly rate to re-compose a yearly salary, and it's not identical. That's not a workplace question, that's a computational inevitability of rounding errors.
Furthermore, mathematics aside, expressing a yearly salary is notably different from expressing an hourly salary. Salaried employees tend to receive a fixed salary with an agreed upon expected amount of hours worked during the year, but small variations in actual hours worked are often not corrected in salary (in informal scenarios, I'm not including things like legally protected on-call bonuses etc).
Comparatively, hourly employees will be paid specifically for the hours they worked, commonly measured by marking the specific start and end times of their work. What they get paid is pretty much regardless of how many hours they were expected to work across the year, it's based solely on the actual hours worked.
yearly rate is 45,000 and appears on the offer letter as such, along with a calculated hourly rate
When you have more than one source of truth, you open the door to those sources being able to contradict one another. Someone messed up here and likely forgot to explicitly point out that one of these numbers is the official number, with the other being an indicative approximation based on that official number.
Educated guess: did someone in HR try to be clever about using one contract template for all employees, both hourly and salaried? It sounds like it.
The answer on how to avoid this is to stop trying to express things as two different units at the same time, thereby avoiding both the mathematical rounding errors and the implied differences between hourly and salaried employees.