Several signs in the Early Cyrillic alphabet are compounds, and the alphabet treats them inconsistently, which is one of the reasons different authorities give different totals for how many letters it had.
Uk is written as o plus the upsilon sign. Yery is written as the back jer followed by an i. The iotified letters, the iotified a, the iotified e and the two iotified yus letters, are ligatures of the glide sign with the vowel that follows it. In every case the compound was originally transparent: a reader could see the parts, and a scribe wrote them as parts.
What happened next differed from case to case. Some compounds fused into shapes no longer analysable, and were then counted as letters, given a name and, in the alphabet lists, a place. Others stayed visibly compound and were counted as spellings rather than as letters. Nothing in the tradition decided the question in general, and the alphabet tables in different manuscripts and different printed books do not agree.
That is why the count of Early Cyrillic letters is given variously in the forty to fifty range depending on the authority. The disagreement is not about what was written on the page, which is well known. It is about whether a fused ligature counts as one letter or two, and it is a question of definition rather than of evidence.
The atlas follows a common convention of listing the compounds as letters, which is what the Slavonic alphabet tables themselves generally do.