Perhaps more at stake aren't practices that display ignorance of mechanical realities but more those that show a contempt for them, and there are plenty of examples of this in the field of motorcycle modification, many more than these few. The first offense that comes to mind in this regard is recammed drum type brake actuating levers. Hondas and other Japanese bikes can run out of drum brake adjustment pretty quickly if the brake is being over-used, partly because they were never meant to be used so heavily, but also because unlike car drum brakes, Japanese motorcycle drum brake shoes are not made "arced," that is, matched in radius, to the brake drum. Consequently, they wear rather rapidly. Inevitably, someone is very likely to attempt to get more miles out of the brake shoes by simply removing the shoe actuating arm and reattaching it one spline over, to get more adjustment travel. What this does however is force already worn brake shoes out even further than nornal on the actuating cam. The problem is, the actuating cam has to rotate more than designed, which puts it dangerously near the 90 degree point at which it can lock. Not a good thing but something I have witnessed many times. With disc brakes being all but universal today, this is now less common, but vintage owners take note.
Similarly egregious a sin is single point mountings. Whether carburetors or exhaust, many a custom machine has one or both bolted up with nary a supporting mount save the the one attachment point. The classic example is the exhaust system that hangs down, usually cut off short, and is bolted on only at the cylinder head. Terrible practice, as it puts undue stress on the cylinder head's exhaust studs. Makes me shudder. Equally bad, maybe worse even, is the use of plastic cable ("zip") ties, especially on fuel lines. I know this is controversial. But remember, I have been in this business over 40 years, and I have seen zip ties fall off, I have seen them over-stress wiring, and worse. To get some outside perspective on this one, I recently had a conversation with a product manager at Alliance Plastics Corp., one of the country's major suppliers of zip ties. She confirmed much of what I had observed. Most are made of nylon and are thus famously sensitive to ultraviolet rays. So much so that in bulk form they are stored in jars full of water to keep them from drying out. The fact is, on a motorcycle, they are constantly exposed to the elements and aforementioned ultraviolet rays, and can become brittle to the point of merely dropping off the frame. Incidentally, only in powersports are these things called "zip ties." Their real name is cable ties.
Though many OEMS do it, aluminum should never be chromed. It just doesn't work, never has, and who knows if it ever will, I don't. Cast aluminum is an extremely dirty metal that is constantly deteriorating. Your chrome hasn't come off yet? It will. It is particuarly inadvisable to decorative chrome plate any close tolerance part such as on a carburetor. The tolerances simply disappear. I once had to use a strap wrench to remove some chromed carb tops. They had obviously been hammered on in order to overcome their poor fit. Ugh!
Here are a few more that could be added to the mechanical bad practice list. Reusing exhaust gaskets, for example, and loosely fitting (usually aftermarket) exhaust parts. Both of these have the result of discoloring the exhaust system and worse, producing annoying exhaust afterburn ("popping"). I would add to this worm drive type hose clamps, because they are ugly, promote overtightening, and aren't too friendly around your hands, Allen screws which while pretty are invariably also overtightened (not to mention also often electrolysis-encouraging stainless steel), and innumerable examples of the improper handling of gaskets. For example, removing gaskets with power tools, and "helping" them with sealers of various kinds. A common mechanical bad practice is putting thread locker on damper rod style fork bottom bolts. Cursing and bloodshed will result when the next unsuspecting mechanic tries removing that bolt without first heating it to dissolve the Loctite. There is a reason most OEMs never did that.
I once worked for a shop whose general manager wanted to give away high performance camshafts as part of a promotion campaign. I was speechless. I mean I just could not believe it. A sales promotion is supposed to produce happier, more active customers, not tick them off. I have written much about how cams should be installed elsewhere on this website, so suffice it to say that the way the typical mechanic (and others) approach cam installation is a very apt example of mechancal bad practice. There is so much that goes into this task that I fear of burdening you, so read about it in my other articles.
Sealers are a subject all to themselves. My rule about sealers is, if there is a gasket, you don't need a sealer (except in extremely rare instances, such as SOHC head gaskets, and where the official manual designates such as on an alternator wire or valve cover cam cutout). Form-a-gasket type sealers are intended for use where the factory did not design a gasket to be used, such as at the crankcase seams of most Japanese engines, as well as the clutch covers and cam covers of later model bikes. But even here, care must be taken. I don't care what anyone says, the factory or otherwise, silicone sealers should never, ever be used on an engine. There are better sealers for engine use, again where warranted (i.e. not to "help" existing gaskets) and these are invariably non-silicone type. The difference is non silicone sealers do not "blob," meaning they don't form "gummy bear" worms. The best engine seam sealer is one that does not blob up, but stays thin, tacky, and level, and is able to be spread very thinly and evenly. Silicone based sealers aren't like this. They blob up, forming after tightening visible "worms" that have no tension with the main body of the sealer and thus too easily drop off (which semi-drying case sealers do not). And think about it. If you have worms on the outside of the cover or case, which by the way are easily removed with the wipe of a cloth, what do you suppose is on the inside, waiting to all-too-easily fall into the engine's oil supply? Say what you will, the use of silicone based sealers is and always has been an obvious mark of unprofessionalism.