The Most likely reason this happens to you is because of Immortal Offering Node.
for example:
Skill 1 deals 90% Fire, 10% Frost damage.
Skill 2 deals 90% Lightning, 10% Rend damage.
you kill a mob with Skill 1 first. You get Immortal Offering stacks, 5x Fire, 5x Frost.
Now Skill 2 deals 60% Lightning, 5% Rend, 17.5% Fire and 17.5% Frost Damage.
Which means that Skill 2 will now apply Lightning and Fire ailments (the highest damage types)
Basically Immortal Offering takes the TOTAL damage of a skill, and adds 25% MORE damage of the element you have stacks of.
It can be confusing. Immortal Offering is INCREDIBLY strong (150% multiplier with 6 ailments) BUT you have to keep this mechanic in mind - It screws with your ailment applications. keep that in mind:)
*Note: Percentages are not exact, they're just an example.