I was unaware skills could actually be put in a queue. As far as i'm aware, the only instance where this could happen is due to skill delay or latency.

For instance, despite you seeing yourself cast an ability, what actually takes place at that time on the server differs from it. The case where you click Transpose after Fire III, but as far as the server is concerned you're still mid-cast of Fire III and your Transpose order does not go through (delayed) till after the Fire III ended on the server. Or visaversa. The cast already ended and transpose went off for the server, but for you your casting animation has yet to end and transpose doesnt happen till after that.

I could be wrong, honestly i could be, but i've been playing BLM for most of the game now and i've never had any of my spells or skills "queue up" so to speak. If i mash my transpose during casting, nothing happens. It's only till after i finish casting that i can use Transpose (it'll be greyed out). Maybe you're breaking something by pressing them together, or very quickly after one another before the server can lock it for the remainder of your cast?