Sometimes we run into problems when we play a series either on the boardgame or on someone else's computer, and then come back to our own computer for a game. The pitchers we just used are not recorded as tired, or pitchers we DID use last game on the computer but have not used since are still listed as tired. The same issue occurs for injuries -- sometimes we need to tell the computer that a player is injured, and sometimes we need to tell the computer that a player is NOT injured.
Eliminating tired or injured status
This is the easy one to deal with. To eliminate the whole team of players being tired or injured, you simply need to give the whole team some "days off". This is accomplished through the Team menu

Then you can simply give your team 15 days off, which should re-set most injuries and all pitchers.

Making players tired or injured
This one is a little more tricky.
First of all, you have to make sure that you have actually started the league, i.e., played at least one game that is a league game. I think that the best way to do this is to always play games by choosing an "Unscheduled game".

Then, be sure to check the "League game" option.

Then play any old game. That will start the league, and then give you the option of selecting some of the menu items that are "greyed out" if the league is not yet started. This is especially important if you play your first games of the season on someone else's computer or on the board game, and then move to your own computer.
Having started the league, you now need to go to the Statistics menu, to Update Statistics.

You'll see that it lists team information at first. You then need to use the down arrow at the top left next to where it says "Team Info" to get a menu with a list of players. Move down the list of players and choose the player in question (batters are listed at the top of the list, pitchers at the bottom).

Having selected the player, use the slider bar on the right to scroll down the options listed. For a pitcher to be tired, you go to the "Days to Next" box, put in the number of games that pitcher needs to rest until he can go again at full strength. Of course, this should be 1 for a reliever who has been used two days in a row, and either 3 or 4 for a starter, depending on whether the starter is starred or not.

One important point here: If you use a reliever in one game, when you go to select a starter for the next game, it will say that the reliever is (Tired-1), as shown here for Rheal Cormier.

However, this does NOT mean that Cormier would be tired if you brought him into the second game. He would only be tired if you brought him in as a starter.
Specifically, the Choose Starter screen will say (Tired-1) after you have used a reliever one day AND after you have used a reliever two days in a row. THE GAME WILL TREAT THE TIRED RELIEVER PROPERLY -- he will only be tired if you bring him in as a reliever a third day running, and this is evident on your team's bench screen during the game. After a reliever has been used two days in a row, he will show up as tired in your list of pitchers. He will NOT show up as tired after one day's usage, even though the Choose Starter screen at the start of the game says he is (Tired-1).
You can confirm this by going to look at the Edit Statistics screen for Cormier in this situation, where it will show that he has 0 days until next.
Injuries
For injuries, you'll want to use the "Injury Days Left" box. This is helpful for our league, where we treat injuries differently than the strat rules in general do.

Finally, if a player has reached the maximum number of injuries for a season according to our rules, and thus cannot be removed from a game for injury reasons, you can change the "Injury Tot Days" to a large number, so that the computer will recognize that the player cannot be injured further.

I have not explored the injury options for bugs as much as I have the pitcher usage options.
That's pretty much it. Let me know if any of this is unclear, or if you find any errors.