This paper presents a critical review of the design of innovation surveys that follow the Oslo Manual standards, based on a series of case studies in Free/Libre Open Source Software (FLOSS) companies. The main objective of the paper is to contribute to identify the specificities of innovation in FLOSS firms that traditional innovation surveys usually omit, to improve current innovation measures and metrics in the software sector. We applied a qualitative analysis based on seven case studies in FLOSS firms from Argentina, mainly through semi-structured interviews to key informants. Such analysis was aimed to elucidate the nature and particularities of the innovation processes and outcomes in the firms, the characteristics of the collaboration with the community and its role in the business model and innovation strategy of the organizations.