It's pretty well understood that N. ordered his execution, immediately after a fair trial of course; that's murder. Hofer was the legitimate head of state of Tyrol, just as much as N. was of France. He was hunted down like a criminal.
It is worth noting that 1809 was the last victory for N. He never won another campaign. The execution of Hofer can be seen as the signal point for the beginning of N.'s decline.
Chasteler, anything specific?
He was ineffective and lost his only battle at Wörgl. The general feeling is that he was wrong to offer himself up for battle in the clear against the French and he paid the price for it. The Tyrolleans did their regular shooting from the hills. Of course, any Tyrollean captured on the battlefield were immediately shot.
It seems that Chasteler was rattled when N. made a decree that Chasteler had committed war crimes -being responsible for the massacre of Bavarians- and was to be immediately shot upon capture. N. also made liberal of use of the Bavarian massacre to pump up the Bavarians soldiers for revenge. It's easy to appreciate N.'s mastery of psychological warfare during Tyrol 1809.
The Austrians were usually completely inept when it came to working with local insurgents and Chasteler was no exception. 1809 was their first and only attempt to appeal to the masses and as we all know it didn't work out very well for them. Their inspiration to attempt it came from news from Spain but the Habsburg army didn't have it in their DNA for guerrilla war. And remember that from the Austrian point of view their army system, although it couldn't handle N. in the field, was, in the end, the winner. Hard to argue with that, actually.
FM Fenner was also there in 1809 and seems to have been a little better at working with he locals but then, of course, he was on home territory.