Noldodan, must be the Confederate Irregulars attacking.
I can tell you that there is one Confederate Irregular at almost every Confederate town in Missouri, all of Conscript strength (their A/D is 6/5, their movement is 1, like a normal unit, and they have -1 HP). The town of Carthage has 4 Confederate Irregulars, 3 of which are Veterans, and 1 is Regular. Confederate Irregulars are "invisible", as are Raiders, Union Riders, and Confederate Guerillas. Conscript has 3 HP, Regular has 4 HP, and Veteran has 6 HP normally.
Home Guards, Garrisons, and cavalry units (except Raider and Union Rider) can detect Invisible units. I suppose I probably should at least put a small Union Cavalry brigade in Missouri somewhere.
2nd Division, Army of Missouri is in Springfield, Missouri, with 3 brigades, which rounds out to 10 HP worth of units for a total of 5,000 men. This is about what Brigadier General Lyons had in June of 1861. The Confederate forces at Carthage, Missouri have 1 brigade of regular troops (McCulloch's brigade, about 2,000 men), 1 brigade of cavalry (I forget the cavalry commander's name, about 2,000 men), and 4 brigades of Confederate Irregulars (Price's Missouri Irregulars, which total about 9,000 men). This is a total force of 13,000 men, under the technical command of Price but actually excercised by McCulloch.
In actual history, Lyons's command was nearly destroyed not far from Springfield, and the remains of his army retreated to Rolla (which by that point was Union occupied). So, what happened to you isn't really far off from what should happen.
I did find one bug though, which has been promptly fixed and a new version will be uploaded fixing it. Home Guard (small) wasn't flagged to detect invisible. The Home Guard in Springfield though is a regular Home Guard and wasn't affected by this bug.
I'm also adding a Conscript Union Cavalry to Brigadier General Pope's command near Quincy, so they can detect the Confederate Irregulars in northern Missouri. As far as I know there wasn't really any Union Cavalry in southern Missouri at this time, so without information proving otherwise, I can't add any down there.
I also have added a Conscript Cavalry unit to St. Louis. And, I've removed one brigade from Fayetteville, Arkansas (which should have been removed, this was an error).
This version will be promptly uploaded, since it fixes a bug.