There's a couple problems with bypassing a fortification. The most obvious is that it leaves an armed force in your rear. Almost every army is heavily dependent on "lines of communication": connections to a friendly area for supply, reinforcements, and communications in the modern sense. These functions are usually quite vulnerable to even a small force, and an army is a prodigious consumer of food and other supplies, which usually can't be reliably obtained in enemy territory. An army marches on its stomach, they say, and without a supply chain an army's campaign is limited to whatever it can carry, which is probably not more than a couple weeks. When that garrison interdicts your supplies, your campaign is in pretty serious trouble. This is one of the principal threats a fortress poses.

Besides raids on supply trains and couriers, the fortress garrison will also be able to seek out and destroy in detail your foraging parties, patrols, reinforcements, and other small units, and then retreat to their safe refuge should you try to respond in more force. In eras of effective artillery, they can even harass you without leaving the fort, which is doubtless situated to command an important road or river. The bypassed force may perhaps even appear in your rear at an inconvenient time, which can be very problematic, or should things go poorly at the front and you need a line of retreat you may find it blocked.

There are times when skipping a fortification (or "pinning it down" with a portion of your forces) makes sense, and there are plentiful examples, but there are many good reasons not to leave it in your rear.

The other problem is more of a strategic than tactical one: what is your objective in waging war? We often think, due to modern circumstances and, well, video games, that the objective is taking land. But in many historical circumstances your need is to destroy the enemy army, and, well, there they are in that hill fort or castle or walled city. You can't bypass them because, well, that's your objective. This, of course, is a huge topic, and I'm not even going to try to get any further into it, though if you have a more specific circumstance in mind I'd encourage asking about that in particular.