The two seventh places combined for sixth overall in Germany with Townley one point ahead of his Suzuki team-mate Kevin Strijbos (Belgium).
"Ben did two solid seven places but messed up qualification and his start place in the gate was not ideal," said Team Suzuki MX GP general manager Stefan Everts.
"Overall I'm happy that he finally finished two motos and I think he needs a few more races under his belt to get better and stronger and to get somewhere in the championship. He is impatient and wants results, so he is not happy," said Everts.
Townley is now 13th in the championship standings as the series moves to Italy this week for the Grand Prix of Trentino.
"It is positive to keep strong for two motos without any major hiccups," said Townley.
"My expectations and what is reality is not the same right now so I'm not happy. My mistake yesterday hurt me for the starts. I had to fight for the top 10 from deep [in the pack] in the first laps and made multiple passes. I made hard work for myself and need to clean up my Saturdays to get in a better place for Sunday."
Italian Antonio Cairoli (KTM) won both races in Germany, leading home Slovenian Tim Gajser (Honda) in the first moto and Russian Evgeny Bobryshev (Honda) in moto two.
Championship leader Gajser posted a 2-4 result in Germany and with seven on the 18 rounds completed he leads with 299 points ahead of Frenchman Romain Febvre (Yamaha) on 291 points and Cairoli on 263.