Ok, riddle me this:
A group of 5 young heroes break into a hobgoblin cave. They're about 3rd level. They take out some grunts (level 3 minion), some soldiers (lvl 3), archers (lvl 3) and a warcaster leader (lvl 3). Each of these challenges are even and appropriate for our young heroes.
The next time they face hobgoblins though, they're 8th level. The DM has two choices:
1.) Re-use the level 3 hobgoblin stats. PCs cake-walk over them.
2.) Up the level of a few hobgoblins per the DMG, then use the Hand of Bane (lvl 8) and Warrior (lvl 8 minion) along with. This keeps the challenge even and allows them another challenging battle with hobgoblins.
Which are you supposed to do?
What's the DM's goal?
Are you showing how the PCs, having gone out into the world and gained power, are now far superior to the foes they once fought? If so, use the level 3 hobgoblin stats.
Or, are you showing how the PCs, having gone out into the world and gained powr, are now facing the elite hobgoblin castes, who have heretofore been working "somewhere else" but have arrived to prevent the PCs from spoiling their plans? If so, use the level 8 hobgoblin stats.
Or, perhaps better, mix the two - have some of the level 3 guys still hanging around, supported by the level 8 guys, and gradually shift the balance as the PCs get closer to the climactic encounter.
I don't see how this is a meaningfully different question than what you'd ask in a 3E game:
A group of 5 young heroes break into a hobgoblin cave. They're about 3rd level. They take out some grunts (CR 1/2 Warriors), some soldiers (CR 1 Fighters), archers (CR 1 Rogues) and a warcaster leader (CR 3 Cleric). Each of these challenges are even and appropriate for our young heroes.
The next time they face hobgoblins though, they're 8th level. The DM has two choices:
1.) Re-use the low-level 3 hobgoblin stats. PCs cake-walk over them.
2.) Add class levels and equipment to the hobgoblins per the MM. This keeps the challenge even and allows them another challenging battle with hobgoblins.
The DMG suggests 2 is the better choice and you should do that since option 1 is clearly a waste of time. The PCs are too powerful for it. However, that suggests a certain design of worldview:
1.) Higher, more powerful hobgoblins have been living in the world, but you encountered only their weak brethren the first time;
2.) Either your hobgoblins become better/tougher/smarter at roughly the same as the PCs or
3.) The PCs really aren't all that more powerful overall. Sure, the PC's numbers increased, but so did the monster levels, the DCs, and the like. Aside from more abilities (aka new powers), the PCs aren't all that different. They're still fighting a hobgoblin with a roughly even chance of hitting it.
Alternatively, you could substitute giants for the hobgoblins.
I don't see this as a bug but a feature, to begin with, and it certainly isn't a bug introduced by 4E.
EDIT:
Continuing, the 4E advice to skip the level 3 hobgoblin encounter makes sense because, in all likelihood, it won't play out interestingly at the table - it's such a cakewalk that the PCs wont need to use interesting tactics, impressive abilities, or, otherwise, much thought to win. And if it's such a foregone conclusion, why waste valuable table time playing it out?
That advice makes sense for the vast majority of cases.
However, sometimes, you want to reinforce how good your PCs have gotten, in which case, playing out 1-or-2 "compstomps" is a good way to drive it home.