Those spots look like a building calcium deficiency. What are you feeding for nutes? Do you have some cal-mag? That's a pretty common deficiency with canna plants so if the nutrients you're feeding don't have enough you can supplement with cal-mag.She should still be living off the cotyledons, so those marks on her leaves (rusty spots) are a little distressing, but I'm not a good enough diagnostician to know why they're there ...hopefully, we can get her growing, then worry about those spots...they may even go away (or stop progressing) once she starts growing a bit...
You said the plant should still be living off the cotyledons, so maybe that means you haven't started feeding yet. If that is the case your plant is telling you to 'get on it.'
And, a magnesium deficiency often comes along with a calcium deficiency which is why they sell them bottled together.