Not fully transparent when exported little white dots around images

I don't know if I should just copy from the illustrator file while in the program and paste into my indesign document directly or export as some other file. I've done the export as EPS before so I went with that. However my images that I drew in illustrator with a brush tool and colored are not full transparent. I see little white spots I don't know if that's because indesign shows them like that or are they actually there. I am combining images because I drew parts separately as opposed to drawing the whole scene together because I wanted to move certain characters/objects/scenery. My question is are the little white spots actually there or is that just that indesign displays it that way? I exported them with the default settings as EPS in illustrator with transparency. I didn't change any settings. Thank you in advance. Oh and I use illustrator cs5.1

so basically only PDF and AI files are able to hold transparency? or are there other formats? In that case what should be a good format for professional print when I have a logo or image that has transparent parts? (In illustrator that would be any part you haven't colored correct?) I've gotten EPS files though that have transparency. Or maybe I'm using transparency wrong I mean like for example you if I made a logo the edges of the logo would be clean but in my case it isn't. there are little white spots as if my background was filled with paintbucket tool in photoshop and removing it with the magic eraser tool from the white background I filled in. I don't mean transparency as in the opacity but as in the background being transparent. Sorry for the confusion!
Example:

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