It's been some time since I saw this movie, but from my remembrance, I believe that Grubitz had become suspicious of Wiesler much before the final search scene. There are several indications of the same:
When Wiesler goes to Grubitz with his report (in a fit of passion after he (over)hears the writer, Dreyman, call the Stasi 'idiots'), he decides not to submit it following Grubitz' casual elaboration of his recent publication on treatment of rebellious artists (Wiesler realizes that Dreyman's whole life might be ruined and his unusual amity for him resurfaces).
Grubitz rightly understands that Wiesler is hiding something from him, although he does not press on this too much. (Wiesler's insistence that the project remain under him also raises Grubitz's suspicion.)
When Grubitz calls Wiesler to the Stasi Prison (Hohenschönhausen) for interrogating Christa-Maria, he asks him if he still remembers where the right side lies (indicating that Grubitz believes that Wiesler's faith in the Stasi's principles is diminishing).
Add to this preformed suspicion the fact:
- that Wiesler left for Dreyman's house much before anyone else.
- that, except for the typewriter, Christa-Maria's information had been accurate (the mentioned flooring was indeed removable and could potentially house the typewriter)
- that there is no sane reason for Christa-Maria to have lied, opening herself up to charges of perjury (she could have insisted on not knowing anything if she did not want to give out any valuable information - why lie and be in more trouble?)
Grubitz is a Stasi officer, and a senior one too. He is smart enough to connect the dots and realize that it was due to an insider that Dreyman was saved from being exposed. That insider, of course, can only be Wiesler, the man in command of the whole Operation Lazlo.