I have finished the quests about the orcs given by general Alix and captain Mitox, but I forgot to report to the general before going to the castle, so I went in using the letter given me by commander Ralph. Then I did the quests for Janus, got kicked out of the castle and went through Elona's dungeons. What I wanted to ask is: if I report to the general now, will this cause any bugs in the game? I am asking this because I was supposed to do this before going to the castle and if she gives me the invitation letter now when I already got kicked out, can this cause any problems?. I read there may be similar situations in the game which cause bugs. For example, I read somewhere that if you don't bring your teleporter stones to the place where they are supposed to be stolen to avoid the theft, this may trigger some bug.

DD is a fairly open RPG and you will complete some quest out of the usual order.
I believe you should continue doing quests. Most of the quest breakers have been patched with a few remaining. I don't remember having any problems with the order of those particular quests. Here is an old list of quest breakers many of which no longer exist. I would keep doing the quests since most can be accomplished out of sequence.
*******Spoilers**********
You might have a problem getting the Dragon armor set if you didn't pick up the Shield of the Dragon while in Stormfist castle (#8). You can still get it but only after getting the pyramid stones back and before you perform the ceremony with the Council of Seven. You can't enter the castle but you can throw one of the stones in the gate far enough to enter. Go around the corner and use the other stone to teleport to the one you threw in the gate. They seem to ignore your presence except at the gate itself. You can then go collect the shield to complete the armor set. I like the armor and wore it from the time I got it to nearly the end of the game. Ignore this if you gathered the shield up while in Stormfist castle.
You can have some dialog for completed quests on occasion but usually it means you have not finished every part of the quest. Look at #3 and see if you have done everything necessary to finish the quest, if not finish it and the dialog option should stop.
Edit: You don't really "throw" the stone in the gate, just walk as close as you can without starting a dialog with the guards. Open your inventory, click on one of the stones and drag it as far into the castle gate as you can and drop it. You can then teleport to it from the other (I go around the corner,don't know why). Teleport out and retrieve the stone the same way you put it in.