0 Ammonia but high nitrite and nitrate!

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Just checked my tank and there were dark green spots on my leaves or possibly brown. I know plants need good subtrate but I really don't want to disturb the gravel until the cycle is complete. There was also holes on my plants ands should I leave them on it trim them off? I also hear that seachem flourish works but dosent work well for swords. The shop owner also used gravel and when I got them there, they looked quite healthy. Please tell me if I should use seachem flourish and what's happening to my plants?!
 
My lighting is 24 in 17 watt 6700k fluorescent lights. I couldn't find anything better near me and the shop owner said this was fine. It is 8t.
 
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