I'm not familiar with the growing cycle of kratom, but as New Wisdom suggested there's but a few reasons a plant will visibly slow down growth. From more to less likely, according to what you mention,
1) Running out of room for spreading roots further. Roots sustain physically the plant structure, and the more they can hold, the higher the plant can afford to grow. Check for signs in the pot (specially, protruding roots in drainage holes) and consider moving it to a larger pot with fresh soil. After a few weeks of root adaptation, it should resume growth. A stem can get thicker as the main root ball develops, but without room to spread, growth will stop. Just think of bonsais.
2) Environmental changes, even if subtle, activate the adaptation systems of plants. This means more resources are spent to adapt morphology, leaving less for steady growth. Growth should continue once the plant has stabilized.
3) Nutrient shortage can slow down growth. Usually that will leave other symptoms either in old leaves, or new growth.
4) Decrease in light.
Mandrake