Nobody designed the whole calendar
Domestic leagues, domestic cups, continental competitions and international football are each run by separate governing bodies, and each has a reasonable, defensible case for the fixtures it schedules on its own terms. The problem is that no single body is responsible for how all of these obligations interact for an individual player who is eligible for all of them simultaneously. A calendar that looks sensible from inside any one competition's own boardroom can look overloaded and incoherent from the perspective of a player who is contracted to appear in most of them across a single season.
Two incentives pulling apart
Every added fixture generates broadcast and sponsorship revenue, which is a powerful and entirely rational reason for competition organisers to keep expanding their offerings, particularly as new markets and formats become commercially attractive. But every added fixture also increases physical load on players, and the medical evidence on injury risk from fixture congestion is not seriously disputed by anyone involved. These two incentives point in opposite directions, and because the body adding fixtures is rarely the body responsible for managing the resulting player welfare consequences, there is little natural mechanism to bring them back into balance.
Why it resists a simple fix
Proposed solutions, from winter breaks to squad rotation rules to reduced competition formats, tend to solve the problem for one stakeholder while leaving it largely intact for another, which is why the debate recurs every few years without a lasting resolution. This is a structural problem rather than a matter of any single administrator making a poor decision, and structural problems generally require coordinated action across bodies that do not share revenue, calendars or incentives, which is precisely the kind of coordination modern football has historically found hardest to achieve.