Hi! I've recently edited the .cue file made by EAC of the CDDA of SOUNDGARDEN - Down on the Upside -1996.
It's a digipack version: 540 526-2 (04). I made a image of the CD instead of separated tracks. When I listen to the tracks separated I notice that they don't start at the beginning of the track. So I putted on the original CD to see if it had the same mistakes, and it does. Now I edited the .cue file so that they could start where they should.
Here's the original .cue file:

PERFORMER "Soundgarden"
TITLE "Down on the upside"
FILE "Down.on.the.upside_1996CD.wav" WAVE
TRACK 01 AUDIO
TITLE "Pretty Noose"
PERFORMER "Soundgarden"
INDEX 01 00:00:00
TRACK 02 AUDIO
TITLE "Rhinosaur"
PERFORMER "Soundgarden"
INDEX 01 04:11:47
TRACK 03 AUDIO
TITLE "Zero chance"
PERFORMER "Soundgarden"
INDEX 00 07:25:74
INDEX 01 07:26:07
TRACK 04 AUDIO
TITLE "Dusty"
PERFORMER "Soundgarden"
INDEX 01 11:44:40
TRACK 05 AUDIO
TITLE "Ty Cobb"
PERFORMER "Soundgarden"
INDEX 00 16:18:45
INDEX 01 16:18:50
TRACK 06 AUDIO
TITLE "Blow up the outside World"
PERFORMER "Soundgarden"
INDEX 01 19:23:72
TRACK 07 AUDIO
TITLE "Burden in my hand"
PERFORMER "Soundgarden"
INDEX 00 25:09:55
INDEX 01 25:09:60
TRACK 08 AUDIO
TITLE "Never named"
PERFORMER "Soundgarden"
INDEX 01 29:59:67
TRACK 09 AUDIO
TITLE "Applebite"
PERFORMER "Soundgarden"
INDEX 01 32:27:40
TRACK 10 AUDIO
TITLE "Never the machine forever"
PERFORMER "Soundgarden"
INDEX 00 37:37:32
INDEX 01 37:37:40
TRACK 11 AUDIO
TITLE "Tighter & tighter"
PERFORMER "Soundgarden"
INDEX 01 41:13:70
TRACK 12 AUDIO
TITLE "No attention"
PERFORMER "Soundgarden"
INDEX 01 47:20:07
TRACK 13 AUDIO
TITLE "Switch opens"
PERFORMER "Soundgarden"
INDEX 01 51:46:72
TRACK 14 AUDIO
TITLE "Overfloater"
PERFORMER "Soundgarden"
INDEX 00 55:39:57
INDEX 01 55:39:62
TRACK 15 AUDIO
TITLE "An unkind"
PERFORMER "Soundgarden"
INDEX 01 60:48:45
TRACK 16 AUDIO
TITLE "Boot camp"
PERFORMER "Soundgarden"
INDEX 01 62:56:60

And here's the edited one [how should I call it? Noncompliant, right?]:

PERFORMER "Soundgarden"
TITLE "Down on the upside"
FILE "Down.on.the.upside_1996CD.flac" WAVE
TRACK 01 AUDIO
TITLE "Pretty Noose"
PERFORMER "Soundgarden"
INDEX 01 00:00:00
TRACK 02 AUDIO
TITLE "Rhinosaur"
PERFORMER "Soundgarden"
INDEX 01 04:11:20
TRACK 03 AUDIO
TITLE "Zero chance"
PERFORMER "Soundgarden"
INDEX 00 07:25:40
INDEX 01 07:25:50
TRACK 04 AUDIO
TITLE "Dusty"
PERFORMER "Soundgarden"
INDEX 01 11:44:00
TRACK 05 AUDIO
TITLE "Ty Cobb"
PERFORMER "Soundgarden"
INDEX 00 16:18:00
INDEX 01 16:18:10
TRACK 06 AUDIO
TITLE "Blow up the outside World"
PERFORMER "Soundgarden"
INDEX 01 19:23:40
TRACK 07 AUDIO
TITLE "Burden in my hand"
PERFORMER "Soundgarden"
INDEX 00 25:09:00
INDEX 01 25:09:10
TRACK 08 AUDIO
TITLE "Never named"
PERFORMER "Soundgarden"
INDEX 01 29:59:15
TRACK 09 AUDIO
TITLE "Applebite"
PERFORMER "Soundgarden"
INDEX 01 32:27:20
TRACK 10 AUDIO
TITLE "Never the machine forever"
PERFORMER "Soundgarden"
INDEX 00 37:37:00
INDEX 01 37:37:00
TRACK 11 AUDIO
TITLE "Tighter & tighter"
PERFORMER "Soundgarden"
INDEX 01 41:13:30
TRACK 12 AUDIO
TITLE "No attention"
PERFORMER "Soundgarden"
INDEX 01 47:19:40
TRACK 13 AUDIO
TITLE "Switch opens"
PERFORMER "Soundgarden"
INDEX 01 51:46:00
TRACK 14 AUDIO
TITLE "Overfloater"
PERFORMER "Soundgarden"
INDEX 00 55:39:17
INDEX 01 55:39:20
TRACK 15 AUDIO
TITLE "An unkind"
PERFORMER "Soundgarden"
INDEX 01 60:48:06
TRACK 16 AUDIO
TITLE "Boot camp"
PERFORMER "Soundgarden"
INDEX 01 62:56:10

My doubt in this is that some tracks have only one INDEX 01, while others have INDEX 00 and INDEX 01... I know that if I change the INDEX 01 the music will start at the time inserted by me, but what about the INDEX 00? Nothing seems to happen when I change that one... But I changed those anyway, just in case... I don't know, what do you think?

I'd say that the problem is with your pressing, not the CUE sheet.

Yes I know that. I said that I had listened to the original CD and it had the same problem. But what I want to know is how should I correct the tracks with both INDEX 00 and INDEX 01 in the .cue file.

There are various ways to correct it but you have discovered that simply substituting a 00 index for a 01 index isn't going to work.

Try an offset correction or edit the 01 indices. Forget about the 00 indices; I suggest removing them altogether if you plan on going the CUE route.

Index 00 values indicate where the "gap" starts. You might notice them on your CD player, when it shows negative values on track changes. They are pretty much useless, so you can aswell remove them. But if you want to be anal about it, adjust them by the same value you adjusted your 01 Indexes.

Thanx for the help, if you look above the two .cue files you can see that I've already edited and changed the values of both INDEX 00 and INDEX 01 on the tracks that have it. And it worked. What I worry about is naming the edited .cue, because I plan on leaving the original .cue and the edited one inside the archive of the rip. Is it right to name it Noncompliant?

An EAC noncompliant cuesheet is made for separated tracks with gaps that were appended to the previous tracks. I don't understand why you would label this cuesheet as such. You can name it whatever you like, of course, but it could cause confusion for anyone else who used the files.

That's what I needed to know. Thank you. I'll just name it 'Edited' then.