Well, that's a miss I guess. I'll try to defend this episode a bit.
I think the Empire's incompetence is a good way of showing that it can be just as inefficient as the Alliance, and even more so, thereby further avoiding the "trains running on time" myth you mentioned. I'm no history buff, but from what I know errors similar to those made by Iserlohn's admirals weren't uncommon in fascist militaries. Stockhausen (Tweedledee) insisting to see the Rosen Ritters in person is stupid, but it's the kind of thing that an arrogant aristocratic officer who is confident in his fortress' defenses would demand. He could also be wary of their communications being intercepted by the enemy (after all, we've seen how deadly and convenient electronic warfare can be in this setting). Besides, they're already next to the control room when security issues start appearing, and by that point he's too impatient to consider them. Similarly, the entire station surrendering seems to me like the consequence of an authoritarian command structure, where the loss or capture of the supreme commander isn't planend for due to overconfidence and crippling when it happens. Same thing with the Admiral's headquarters controlling most of the station and the Thor Hammer.
As for the Rosen Ritter being imperfect infiltrators, well, Von Schönkopf and his pals' experience of Imperial life might be limited, but it's still the best the Alliance has. (Alliance and Imperial infiltrators appear very uncommon in LoGH due to the difficulty of travel between the two nations, with only Fezzan having an elaborate spy network). And they definitely needed to take Stockhausen hostage in order to seize the station intact, otherwise he could've tried to escape while the zealous security officers would fight the infiltrators, which easily could've resulted in the control room being destroyed.
Regarding the 13th Fleet's jamming abilities, my best guess is that they were able to outmaneuver the garrison fleet and place themselves in a way that allowed them to cut off the enemy comms. The garrison probably noticed that they were cut off from Iserlohn, but Seeckt (Tweedledum) continued the search partly because he's an overconfident idiot who hates Stockhausen, and partly because losing comms in battle seems common in this setting. I'll concede that the way jamming works is very vague and plot-dependant though (I have some headcanons to justify it, but most of the time it really just seems to happen karmically to the commander who's doomed to lose the battle).
Then there's Seeckt's charge at Iserlohn, which I think is a really powerful scene that embodies one of the series' themes : egocentric leaders sacrificing millions of people in order to further their goals, whether it's Seeckt's bullshit "warrior's honor" philosophy, Reinhard's megalomaniacal conquest of the stars, or so, so many others I can't talk about yet. In that precise case, it's a much-needed rebuttal of the trope where fanatical soldiers of an Imperial power die to the last man in a futile assault, which is sometimes portrayed in an uncomfortably glorified way. It's a refreshing message for a mil sci-fi work and an anime, and I think it's one of the points where LoGH truly shows how superior it is as a war story compared to, say, Starship Troopers (the book) or GATE.
...okay, that was more than "a bit".