When an ism maqsur consists of three letters, its final alif represents an original letter. In the dual, that original letter returns.
عَصًا → عَصَوَانِ
The returned original letter is waw.
فَتًى → فَتَيَانِ
The returned original letter is ya.
Therefore, do not turn every three-letter maqsur ending into ya automatically; the dual reveals whether waw or ya returns.