I got told by this notification for replying to a linked thread is I had no idea that the thread was not allowed to have links on it.
Anyways this notification pops up telling me to try and get the links removed. I didn't make the linked thread so why Am I getting the penalty? Can this problem be solved or fixed? I did nothing wrong.

I am confused Penalty? What thread were you trying to reply in? I checked all your posts within the last 5 days and don't see any links in any of them. I checked all the threads you started and they also don't provide a clue.

As a new member, you are limited for a time from posting any outside links. This was implemented to prevent spammers from adding links, perhaps that is what you mean? If so, after a certain time participating in threads, that restriction is automatically lifted.

If you are replying in this thread The thread "Identify this daisy?what kind of a daisy is this?" in Plant ID forum
where one member added two links, do not 'quote' their post, as it adds those links into your post. Since you are currently in the restricted time frame, it automatically treats it as links you added because they are within your reply. Just address the member without quoting.

Calif_Sue said:If you are replying in this thread The thread "Identify this daisy?what kind of a daisy is this?" in Plant ID forum
where one member added two links, do not 'quote' their post, as it adds those links into your post. Since you are currently in the restricted time frame, it automatically treats it as links you added because they are within your reply. Just address the member without quoting.

It's all good the problem has been solved! Just the problem is no one knew about this.
All is good!