Are Dortmund a poor club by any chance? That is the only logical reason i can think of them offloading 2 of their best players to their major rivals.
They will reach at least 250 Mil € annuall revenue without transfers at the end of the season, including transfers they will break the 300 Mil€ line if Lewandowski leaves in the summer.
They are financially in extreme good shape and quite comfortably the 2nd richest club in Germany behind Bayern.
Their biggest problem is, that their financial growth was so fast (150 Mil€ in 2011, 200Mil € in 2012), that they have outgrown their own contracts and their wage roll is really small in relation to their financial ressources.
Götze signed his last contract in spring 2012, which included the 37Mil€ buy out clause and an annual salary of around 4Mil €. Bayern Munich offered him 12Mil € (this is slightly less than what Rooney gets at United), which makes him their top earner instantly.
Lewandowski simply did not want to renew his until 2014 running contract, which is why he still earns so little money. He or better his agent Kucharski wants to make him the biggest brand in Polish football history, which is why he wants to go to Bayern aswell. Dortmund was actually ready to offer him nearly as much as Bayern in terms of salary.
The officials of Dortmund are already working on closing the big gap between revenue and wages. A lot of their players renewed their contracts in the last six months, some of them only for one more year (e.g. Bender and Pisczcek), which are basically wage rises.
Kuba is set to renew his current contract until 2018 in the next days, Gündogan is also right now in talks and things are looking really good. They also want to sit down with Reus in the summer and want to get rid of his buy out clause of 35 Mil€, which could come into effect in 2015. I also expect talks with Hummels to give him a raise including a renewal until 2018 like Kuba.