With your setup, you shouldn't have any problems with penetration, but I agree your shot placement is not the best. That aside, I think you have some tuning issues that need to be addressed. So let's start at the beginning and work our way up from there.
1) Lets get your bow close and then fine tune it. With a draw board, verify your draw length and that the cams are hitting the stops at the same time. For Hoyts 3 years old or older, having the top cam hit first by 1/16th to almost an 1/8th inch is okay. For your Matthews, you would want them hitting at the same time. If you don't have a draw board, find a shop that does or build one yourself. If you have a press, you can adjust the timing and sync of your cams at this point. If you don't have a press, find a shop that is willing to work with you. Verify that your arrows are the correct spine and length for your setup. Use Archer's Advantage or OnTarget2 software to fine tune your arrow build. If in doubt, go heavier on spine and weight.
2) Centershot and nock height. Set your center shot so that if you ran an arrow against the riser parallel to a nocked arrow on your rest, they would be indeed be parallel. A tiny clamp to hold the arrow to the riser helps. I don't know the optimum setting for a Matthews, but for a Hoyt it is about 13/16ths from the riser. For nock height, it is always a great place to start with your arrow running level.
2) French Tune/Modified Walk Back Tune: Get yourself a target and set it on a stand so that it is at shoulder height. Run a plumb bob line down the center of the target. At 6ft with your bow level with the target, try to put an arrow through the string. Adjust your sight until you are putting arrows perfectly through the string. That sets the base windage on your sight, now we need to adjust your base centershot to how you shoot. Back up to 10 feet. Try to split the string again but make adjustments with your rest. A little goes a long way. You should be pretty darn close without any adjustments, if you are, back up to 10 yards, and fine tune your centershot by making very tiny adjustments to your rest. If this were a Hoyt, I prefer to adjust the yokes, but you get the picture. Now would be a good time to also rough in your sight pins.
3) Bareshaft tuning. Don't do this unless you have great repeatable form or you will be chasing your tail. If you are primarily a hunter, then skip this step and proceed straight to broadhead tuning. Using the same target at shoulder level, pick a dot and shoot one fletched arrow. Make sure it is a good release and the shot feels good to you. Now strip the fletching off another arrow, and shoot it at the same dot. Are they grouping together? Is the bare shaft hitting the target straight? On a bow with yokes, if the arrow is slightly right or left and high, put a 1/2 twist in the same side yoke that you want the arrow to move. This will move the POI down and over. If you need to move POI left or right only, take 1/2 twist out of the opposite side you want the bare shaft to move and 1/2 twist into the side you want it to move. If the arrow is low, add twists to the control cable. If the arrow is high, add twists to the buss cable or equal twists to each yoke end of the buss cable. For binary cam bows, as long as you are reasonable close in POI with bare shafts and fletched arrows, make very very very tiny adjustments to the rest. If you are off by a lot, it is time to shim the cams and a good shop can help you with that. If you can't get your bare shafts to move the way you want them, then you have arrow spine issues. Either reduce point weight, add weight to the back end, or pick a heavier spine arrow.
Broadhead tuning: At 10 yards, pick a spot. Shoot one fletched field-point tipped arrow. Retrieve the arrow and mark the POI with a piece of tape. Repeat with your favorite broadhead. If it hit the tape, you are good, back up to 20 yards and repeat. If not, make super super tiny adjustments with your rest. If your broadhead tipped arrow is way off, you may have an arrow spine issue or sloppy form. Repeat again and only count shots that feel good. Once you have broad heads hitting with field points, go ahead and backup and verify that your broad heads fly true at your maximum effective range.
Fine tune the sight and the shooter: Don't get close, get perfect. You just fine tuned your bow, if you miss.......you are to blame. Practice, practice, practice and figure out your maximum effective range. Get those pins perfect. Get your second and third axis perfect. Get good enough that robin hoods become a regular thing if you stupidly shoot groups at anything less than 30 or 40 yards. Know for a fact that if you have an animal giving you a good shot opportunity at anything less than your max effective range, you will be having fresh meat for dinner. BE CONFIDENT IN YOURSELF AND YOUR EQUIPMENT.
