Usually, the alignment module processes the files to be aligned and suggests the result to the user. The user can either accept this result (in this case the alignment would have been automatic) or verify the alignment result by examining it segment by segment and manually correcting mistakes like the one shown on the previous page (manual alignment).
Since misalignments of this kind are quite normal and since often it is necessary to translate one source segment by two or more segments in the target language, or vice versa, manual checking is usually recommended, so that the results to be imported into the TM are as "clean" as possible.
Nevertheless, care should be taken not to spend excessive time on achieving perfect alignment. The alignment tool is a productivity tool. The goal is to populate a translation memory database as quickly as possible with valid translation segments, not to achieve perfect alignment of all source and target texts. Therefore, in practice it is common to ignore very complex misalignments.