Digital clinical decision support algorithms (CDSAs) that guide healthcare workers during consultations can enhance adherence to guidelines and the resulting quality of care. However, this improvement depends on the accuracy of inputs (symptoms and signs) entered by healthcare workers into the digital tool, which relies mainly on their clinical skills, often limited, especially in resource-constrained primary care settings. This study aimed to identify and characterize potential clinical skill gaps based on CDSA data patterns and clinical observations. We retrospectively analyzed data from 20,085 pediatric consultations conducted using an IMCI-based CDSA in 16 primary health centers in Rwanda. We focused on clinical signs with numerical values: temperature, mid-upper arm circumference (MUAC), weight, height, z-scores (MUAC for age, weight for age, and weight for height), heart rate, respiratory rate and blood oxygen saturation. Statistical summary measures (frequency of skipped measurements, plausible and implausible values) and their variation in individual health centers compared to the overall average were used to identify 10 health centers with irregular data patterns signaling potential clinical skill gaps. We subsequently observed 188 consultations in these health centers and interviewed healthcare workers to understand potential error causes. Observations indicated basic measurements not being assessed correctly in most children; weight (70%), MUAC (69%), temperature (67%), height (54%). These measures were predominantly conducted by minimally trained non-clinical staff in the registration area. More complex measures, done by healthcare workers in the consultation room, were often skipped: respiratory rate (43%), heart rate (37%), blood oxygen saturation (33%). This was linked to underestimating the importance of these signs in child management, especially in context of high patient loads at primary care level. Addressing clinical skill gaps through in-person training, eLearning and regular personalized mentoring tailored to specific health center needs is imperative to improve quality of care and enhance the benefits of CDSAs.