Many thanks for your precious reports ^.^I will fix everything in the next update. (Random freezes are hard. Do you happen to remember if the game screen was freez but the game kept "running" or if it freez completely?)
Currently the only way to increase your affinity beyond level 2 is to interact with the golden treasure chest indicated by the arrow, on the map with the large lake (you will have to use the blue Kelsy to go around from above).
I hope for the next update to also add the lv up of the normal affinity: like you did, after reaching the max in the current affinity you have to talk to Ajoora "press T" and select affinity. The first time she will ask you to complete a request or answer some questions before increasing your affinity ; )