Argument Exception "Item with Same Key has already been added"

This error is fairly self-explanatory. Dictionary keys are unique and you cannot have more than one of the same key. To fix this, you should modify your code like so:

Dictionary<string, string> rct3Features = new Dictionary<string, string>();
Dictionary<string, string> rct4Features = new Dictionary<string, string>();

foreach (string line in rct3Lines) 
{
    string[] items = line.Split(new String[] { " " }, 2, StringSplitOptions.None);

    if (!rct3Features.ContainsKey(items[0]))
    {
        rct3Features.Add(items[0], items[1]);
    }

    ////To print out the dictionary (to see if it works)
    //foreach (KeyValuePair<string, string> item in rct3Features)
    //{
    //    Console.WriteLine(item.Key + " " + item.Value);
    //}
}

This simple if statement ensures that you are only attempting to add a new entry to the Dictionary when the Key (items[0]) is not already present.

As others have said, you are adding the same key more than once. If this is a NOT a valid scenario, then check Jdinklage Morgoone's answer (which only saves the first value found for a key), or, consider this workaround (which only saves the last value found for a key):

// This will always overwrite the existing value if one is already stored for this key
rct3Features[items[0]] = items[1];

Otherwise, if it is valid to have multiple values for a single key, then you should consider storing your values in a List<string> for each string key.

For example:

var rct3Features = new Dictionary<string, List<string>>();
var rct4Features = new Dictionary<string, List<string>>();

foreach (string line in rct3Lines)
{
    string[] items = line.Split(new String[] { " " }, 2, StringSplitOptions.None);

    if (!rct3Features.ContainsKey(items[0]))
    {
        // No items for this key have been added, so create a new list
        // for the value with item[1] as the only item in the list
        rct3Features.Add(items[0], new List<string> { items[1] });
    }
    else
    {
        // This key already exists, so add item[1] to the existing list value
        rct3Features[items[0]].Add(items[1]);
    }
}

// To display your keys and values (testing)
foreach (KeyValuePair<string, List<string>> item in rct3Features)
{
    Console.WriteLine("The Key: {0} has values:", item.Key);
    foreach (string value in item.Value)
    {
        Console.WriteLine(" - {0}", value);
    }
}

If you want "insert or replace" semantics, use this syntax:

A[key] = value;     // <-- insert or replace semantics

It's more efficient and readable than calls involving "ContainsKey()" or "Remove()" prior to "Add()".

So in your case:

rct3Features[items[0]] = items[1];