This is not a "problem". It is just the way things are with martagons. Why are some people short and some people tall? It's likely genetics, and neither person is defective. Just as you have heard that some plants (not lilies) are more difficult to transplant than others, so it is with lilies, and martagons require more care. Sometimes martagons need extra time (even an extra year) to recover from the trauma of storage out of the ground and transplanting.
Of yours, if one(s) that grow well and one(s) that are "dwarfed" are the same cultivar (a named variety, like 'Pink Attraction'), and they are growing with the same conditions - soil, water, light, fertilizer, temperature, then the difference is most likely caused by unnoticed physical damage at the time of planting. Or, it is pathogen induced - rot, disease, virus.
If they are different named matagons, or just labeled as martagons (thus, likely seed grown), then the difference is probably attributed to genetics. Seed grown lilies are especially variable; some are just runts, or naturally take longer to mature.
Two seed grown martagon lilies: same age, same parents, same seed lot.
Two Lilium monadelphum plants: same age, same seed lot, wild seed.
